View source for Converting to 4.0L cylinder head, EFI and cam - manual transmission

By AMC Eagle Nest member tougeagle

This article is under construction until further notice. It Will be up soon!


A few have requested a writeup on my build, and now that the important things that make the car move are good to go, it's time. I will say that I am occasionally updating this with later information as I work some of the bugs out that have developed. None of them are internal engine related or a problem directly associated with this type of swap, but rather in parts choice or my choice to shortcut something I shouldn't have.

In my personal opinion, this conversion is the single best thing that could ever happen to an Eagle. All of the negative stereotypes that ,come with Eagles center around their looks, and their less than stellar reliability, thanks to the archaic technology under the hood of these beasts. And while not much can be done about the looks (this why we're unique in the classics world), the engine is an entirely different story. With the advent of fuel injection, AMC was one of the last companies to use carburetors on their vehicles, and it's part of what caused them to get left behind. This conversion, if done correctly and with all parts listed, WILL give you the power gains you could only dream about with a carburetor. My baby is much faster, more efficient, more capable, and far more reliable. I've put 3300 miles on her since the conversion, and the only glitch was the rear axle, thanks to my own ignorance on differentials, and a loose injector connector. Out of this swap I also attained an AX15 and NP249 full time + 4low w/center locking diff. I have tons of low end and top end power, when I need it for city or highway driving. I've pulled 2000 lbs a couple of times without a problem, at 70 mph.

This writeup is for manual transmission Eagles NOT equipped with AC. If you want to retain your automatic and/or AC, unfortunately you will need to do some slight additional research, as my car came stock with neither of these.

If you plan to do this conversion, consider doing the gear train swap as well, it in most cases, won't cost much more than the stuff He$co carries, but you'll see far greater benefits. I did not use ANY Renix parts, nor would I recommend it, you'll go through the same effort for less power.

As much power as this conversion makes, I would STRONGLY recommend, from my own experience, that you make absolutely certain your engine is in good condition (whether it runs right or not), before doing this. Check compression, bearings and valve train components for any abnormal wear, and again, get rid of the plastic timing gears!

The parts list. All prices are junkyard or ebay unless specified. This list is for manual transmission vehicles.

1992 4.0L with cylinder head, manifolds, coil, distributor, valve cover, cam, spun rod bearings - 20$ from craigslist
However, that was a VERY lucky shot, so in most cases, expect these prices...

91-95 4.0L cylinder head (casting 7120) 250$ includes full machine work and price of the head, @ 50$ for the head

91-95 Cam, lifters and push rods (higher lift and duration than the later dual pattern cam, a major plus with our larger displacement) 10-50$

91-2005 intake manifold (I used a 92, however the 98 and up equal length manifold will net an extra 5-10 hp) 10-20$

91-2000? exhaust manifold, single outlet. 10-20$

Head bolts, mine were 100$ from [http://www.headbolts.com], as they are 7/16". The 1/2" bolts are half the price. 


91-95 Engine computer, match to transmission type. You can use OBDII (96 and later), though I'm not exactly sure what the wiring differences are, other than the extra O2 sensor. 10-50$


93-95 wiring harness. Avoid the 91-92 harness, they tend to have corrosion problems. This should include the relay box (PDC) and battery cable. 10-50$. Mine was 65$ from craigslist, included PCM and PDC.


Water soluble packing peanuts 5$


JB weld, the BIG tubes 10$


Bosch 044 external in-line fuel pump. THese are capable of 80 gph @ 70-90 psi. I used a Hesco pump, and am somewhat regretting it. They're only 40 gph. 180-200$ shipped from Ebay


7 amp alternator diode from Hesco 12$


45k volt 4.0L ignition coil 45$ shipped from Ebay


93-98 distributor 10-20$

O2 sensor 40$ from ebay

Chevy small block fuel pump block off plate. 10$

91-up flywheel 50$ from ebay

73-76 V8 CJ pilot bushing, 5$

96-up AX15 transmission (.75" input shaft tip, external slave bellhousing) 290 dollars with 30 day warranty on all parts 
from J &B autocrushers in Commerce City, Colorado, included all clutch and shifter hardware except for pressure plate and disc

late 90s/early 2ks Dodge Dakota AX15 shifter (they came behind the v6 models) 40$ with knob and hardware

98 Grand cherokee transfer case, NP249, 100$ Western Auto Recycling, Federal heights, CO

New clutch kit 110$ from Ebay

Advanced Adapters CJ/YJ plastic to metal braided steel hose with fittings +- 65$

8 feet of Goodyear J30R9 FUEL INJECTION hose +- 40$. DO NOT USE REGULAR FUEL HOSE. It will burst under the pressure of an efi fuel system

2.25" J-bend mandrel bend exhaust tube, 35$ from Ebay

10' 2.5" OD exhaust pipe 40$ from Meineke

2 Walker catalytic converters, 2.5" 140$ Advance Auto Parts

Energy suspension poly sway bar end link bushings, 14$

93 Dodge Dakota v6 speed sensor two wire 5$ Western Auto Recycling, Federal Heights, CO

Pipe bushing 3/4" outside x 1/2" inside 4$ Hardware store

Wilwood remote reservoir for clutch master 60$ Summitracing.com

94-95 valve cover 10$. Make sure to find one with fittings if you can, they're getting scarce at parts stores. Ebay

4.0L Full Fel-pro gasket set with ONE PIECE oil pan gasket +- 90$. DO NOT get the multi piece gasket. They're crap.

O2 sensor bung 5$ Summit Racing

3/4" square tube steel, approx 3', 10-15$

Hi flow thermostat, 195 deg _ONLY_. 12$

Ford Racing 24lb/hr rebuilt refurbished fuel injectors 110$, though I recommend 26-28lb injectors if using return system with stock fuel pressure regulator

Adjustable fuel pressure regulator 50$ Ebay

(2) 2" conduit clamps (for fuel pump) 5$

91-95 Throttlebody 10-50$. I hand-bored mine out to 60mm. If you are using a 96 or later system, use a 96 or later tb, due to vacuum fittings for purge solenoid system.

Returnless fuel rail (96-up) 10-20$

Charcoal can (91-95 only) 10-20$

4.0 Thermostat housing, with two wire coolant temp sensor 10-20$

93-96 crank position sensor (if using 91-92 harness, use same year crank and cam (distributor) sensors) 5$

Scoche positive battery terminal connector, 4-wire 10$ Wal-mart

4.0 Starter 10-60$

2' 1/4"x1" strip steel 10$

4 new forged u-joints 40$

1 Collector to cat pipe section from XJ cherokee 10$

Cherrybomb glasspack 25$

2.25"-2.5" exhaust flare kit from Summit, get the two flare kit, will come with street hookup kit, 15$

Autozone 3" intake tubing and cone filter: 75$

two main transmission bolts (side of the block) 1/2" longer than stock, this greatly aids in installing the trans back into place

A decent multi-meter

Recommended:
Box of assorted Grade 8 bolts, US/Euro models, unless you're organized enough to keep every single bolt
Double or triple roller timing chain set, if you haven't replaced those plastic gears, NOW IS THE TIME.


This was the final stage of my engine bay before the conversion:

65k volt HEI system, motorcraft 2100 conversion. It still would not pass emissions, and though there was SOME power gain, I didn't feel it was worth the 450$ I had spent on it.

So, off came everything, down to the head:

The old 258 head. The engine had been recently rebulit, but not very well, as I had to replace the rear main and the oil pan gasket, well before I had torn it down. The 258 head ports are much smaller than the 7120 casting 4.0 head ports, and all are on an equal plane. The 4.0 intake ports are higher up, and give a softer angle into the cylinders, while the 258 head ports are very nearly 90degrees. The less angle into the cylinders, the higher the velocity of gasses in and out.
The 4.0 head:

This was after glass beading and magnafluxing, but before machining. I would HIGHLY suggest getting the head cleaned up, planed flat, valve stem seals replaced and a 3 angle grind on the valves. You could just slap the junkyard head right on after scraping it, but if the valve stem seals are bad or the head is warped, you will have created much more work for yourself than its worth.

The intake manifold... At the time, I had 19lb/hr injectors on it, which did alright, but the car still ran far too lean.


Engine torn down:

If you have a bad water pump, or plastic gears, or bad rear main/oilpan gasket, NOW is the time to replace them. There is much less weight on the engine, and it will make it easier to lift and balance, and make everything much easier to reach. If you must replace your timing set, NOW is the time to remove your 258 lifters and cam, and install the 4.0 cam and lifters. The lifters must match the cam, same with the pushrods. You will have to remove your radiator to get a puller in to remove the harmonic balancer.

You will need to tear it down this far. While it is at this stage, grab the replacement transmission and transfer case, and install them. It's MUCH easier to get to all of the bellhousing bolts. If you're going from a T5 to AX15, you'll need to use the AX15 bell cover. As stated earlier, replace the two bolts on the side of the block holding the trans to the block with ones a half inch longer, it will greatly aid you in installing the transmission, making that last 1/4" of distance a breeze.
The parts:





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I wish I had pictures to show the flywheel differences. The 4.0 flywheel sits at a different distance from the engine compared with the 258 flywheel, which will cause clutch engagement issues, so if using an AX15, the 4.0 flywheel MUST be used. Also, you MUST use a 4.0 starter if you use a 4.0 flywheel, as the ring gear is closer to the engine, and would not allow the 258 starter to disengage. If you are going to retain your T5 or other trans, then you can go with the hesco cps unit, of course. However, if you're doing an AX15 swap, forget about it because you'll already have all the components you'll need other than the sensor itself. The 4.0 flywheel has notches in it that are read by the sensor through magnetics, they're the crank sensor trigger.

If you did not cut out the rest of your pulse air system and exhaust, do so now, it will make this part much easier.
Make sure to leave all differential brackets from block to axle in place.
If you do not have a transmission jack, use two hydraulic jacks with wheels, and place one directly under the bellhousing and the other slightly offset on the transfer case, to balance everything out. Rock the trans back and forth to get it out/in at the transfer case output, raising your jacks up every inch or so of progression if going in, lowering if going out. Make sure to grease the inside of the throwout bearing where it slides along the input shaft sheath, and grease the shaft splines and pilot tip as well. You MUST use the alignment tool when putting the clutch and pressure plate together, or you will not be able to get your transmission fully installed. You will have to support it with a jack after it is installed while fabricating/modifying the transmission mount.

I do not currently have pictures of the starter wiring, but it's easy. The 4.0 starter uses a positive battery cable instead of negative. Hook it to the terminal or the scosche terminal for the positive side. The green/black wire coming from the starter goes to the ground/negative side of the starter solenoid. Remove ALL red wires from that side of the starter solenoid, as any voltage going to that side that should not be there will cause the starter to remain engaged after the engine is started.

Flywheel in place:


Here is the difference between the V8 CJ pilot busing (left) and AX15 4.0 pilot bushing (right). The 4.0 bushing WILL NOT fit, the outside diameter is too small.


Ax15 clutch arm and throwout bearing:


Remote reservoir kit/clutch master + slave cyls/metal clutch line:


Here is how I fabricated the transmission mount:






The NP249 will bolt right up to the AX15, in most cases. I've heard that some years the input shaft  protruded different distances, so stick with 98.
Also, you can use the slip yoke from the transfer case, and install it to the end of your Eagle driveshaft. It may cause some driveline vibration, but that's something I'm still kind of working out. I just can't afford a custom length driveshaft right now. It will make it driveable but there will be vibration at highway speeds.

The stock Eagle speedometer gear will work in the transfer case, and it is accurate. However, the 249 gear should swap over, though I haven't confirmed this.  The cable is a tight fit, but it WILL fit and it shouldn't suffer any damage.

Now that the driveline is in place, it's time for the really fun stuff.

The AX15 (or auto trans) bellhousing has a location for the stock crank sensor. Bolt it up after mounting the transmission to avoid damage to the sensor. If you do this before mounting the manifolds it makes it easier to get to.

If you did not previously swap out the cam, it's time. Remove your radiator, outer crank pulley, and all belts. Use a harmonic balancer puller to remove the balancer. Set your 4.0 lifters in a bucket of clean oil. Open the timing cover, and zip tie the chain to the cam gear. DO NOT remove the chain from the crank and cam gears, or you will have to retime the engine. Remove the cam gear from the cam. Use a pen magnet to pull the lifters out of the block, there is nothing else holding them in. Slowly pull the cam out of the block, there is nothing else holding it in, but make sure you have set your timing chain and sprocket out of the way. If it makes it easier, use a Sharpie or Whiteout to mark the chain and crank gear, if you must remove the chain. Thoroughly oil all bearing surfaces (lobes included) of the 4.0 cam, and VERY SLOWLY slide it into the block, being very careful not to let it catch an angle, as you risk damaging the cam bearings in the block, until it is flush in the block. It will sit exactly as the 258 cam did. Carefully install the 4.0 lifters into the block, they will slide right in. They must go straight down or their surfaces risk damage from the sharp edges of the lifter bores. If you marked and removed your chain, reinstall it on the crank sprocket EXACTLY how you took it off. The 4.0 cam and 258 cam both share the same position of the dowel pin for the sprocket. Slide the sprocket onto the 4.0 cam. This might take a very, VERY light tap with a mallet, as the dowel pin on the 4.0 cam may be just half a hair larger, but it WILL fit. Then, install the cam bolt. You will have to put the car in gear to keep the engine from turning too much while you tighten the cam bolt down. Reinstall the timing cover after replacing all associated gaskets, and install the crank damper. DO NOT hammer the damper onto the crank, use an installer to push it  back onto the crankshaft.

Now it's time for the head.
Make sure to scrape your block surface completely clean with a flat edge razor blade, and avoid getting anything in the cylinders. While the head is off, you can inspect your cylinder walls.
You will need to fill the water jackets on the MANIFOLD side of the head, the triangular shaped ports, there are three surrounding each stud hole. DO NOT fill the two larger water jackets at the back of the head, as the block is mostly closed deck, and closing those two ports will not allow coolant to flow through the head.

Stuff the water jackets with two or three peanuts, making sure they will make a firm base, and a completely closed area within each jacket. Make sure there is approximately 1/4" depth in each.
Mix up your JB weld, but only after stuffing the head, the stuff will set up fast.
Use a plastic knife to dab the JB into each of the stuffed jackets. If it flows down further into the head, pull the peanuts out, wipe up the mess, and restuff the jackets. You don't want to fill the water passages inside the head. Do not overfill the jackets or you will have to re-plane the head.
Let the JB weld set up overnight, give it a good 24 hours. Do not expose it to any water or solvents during this time. Whlie it is still wet, you can scrape excess away from the jackets with a razor blade. If you do not plan to run your engine for a few weeks, or it has been sitting open for more than a week, coat the cylinder walls with a layer of clean oil.

After the head has fully cured, place the head gasket on the block. You'll notice how most edges of the gasket will match up directly with the block. Have someone help you slowly position the head onto the block, on top of the gasket. Be VERY careful not to crease any corner of the gasket, or let the bare head come in contact with the block, any grit left behind can gouge the mating surfaces. The head weighs 70+ lbs, you WILL want to have help to get it right. I did it myself and I went through two gaskets in the process. Once the head is on the block approximately aligned, use a flashlight and very very gentle nudges on the edges of the head/block deck to match up the head and gasket to the block. The easiest way to do this is line up the stud holes first, then make sure you have a consistent amount of gasket edge on each side of the head. The gasket. After you have aligned your gasket completely, with the head, install the head bolts, but DO NOT TORQUE THEM! If your engine uses 1/2" head bolts, they will also help align the gasket. Once all are installed and hand-tightened, it's time to torque the bolts down.
The pattern looks like this
13     14  BACK
9       10
5       6
1       2
4       3
8       7
12     11 FRONT
Torque the bolts to the 258 specs. DO NOT torque them to the 4.0 specs, you will stretch your block and cylinders out of round, unless your engine was bored to those specs with a torque plate. Coat #11 with RTV on the SIDES of the bolt only, using a thick bead. The point is not to seal underneath the head cap, but to seal the chamber, because some 4.0 heads have a casting opening in the cooling passage, in that chamber. The torque pattern is a spiral, starting with 1 on the left and moving clockwise. Torque all bolts to 40lbs first, then to 65 lbs, then to 85lbs. It should look like this installed:


Notice the port differences I was talking about earlier....

Now that your head is installed, you will need to let the RTV cure on that #11 bolt, but don't worry, there's plenty you can occupy yourself with in the meantime.
Install your 4.0 pushrods, and rocker arms. The 4.0 and 258 share the same rocker arms, so if you wish to carry yours over, you can. Be VERY careful not to distort the rocker arm bridges when tightening down the studs. You can then install your valvecover, if you wish.

Time for the manifolds. JUST KIDDING! It's actually time for the front diff bracket. This has always been a topic of discussion regarding a 4.0 head swap because the 4.0 manifold is blocked by the stock bracket. Well, that's easy enough to fix. Remember that 1" wide steel strip and 3/4" square tube? You will use this to make a custom diff bracket. The goal is to get the bracket as low-profile and close to the block as possible. The easiest way to do this is with a bench vice. I can't quite explain in words how to do it, you just have to go through a little trial and error. It should look like this when you're done:


In the first picture, the right side is the block side, the left is the diff side. It will generally match the shape of the stock bracket, but instead of the holes of the bracket being angled, the bracket itself will be angled. This will allow the exhaust to completely clear it.

Well, now what? More JB weld...
Instead of spending entirely too much money on a new speed sensor from hesco, grab yourself one from a cherokee with cruise or a mid-nineties dakota. The sensor should look exactly like the hesco sensor. Mix up a batch of JB weld, and grab your pipe bushing. Remove your instrument cluster, and screw the bushing to the back of the speedometer. It should be a perfect fit. Coat the outer, exposed threads with JB weld, and place the large end (transfer case side) of the speed sensor on the bushing, making sure the small thin rod protruding out is snugly inside the back of the speedo, it's the link between the cable and the cluster, and is EXTREMELY important. It's just tight enough the threads will catch, but loose enough the threads will not hold, so this is necessary. Position the cluster upside down so the sensor can sit on the bushing and allow the JB weld to dry.
The parts:


Bushing on cluster:

Sensor/bushing installed:

We will come back to this later. DO Not install it yet.

You still have a few hours to go, so it's time for the manifolds. First, you will need to cut your power steering bracket down. Take off the top hole, all the way to just above the second from top hole that bolts to the manifold. Get as much of the bracket on the block side of the pump as you can without destroying it, as the 4.0 exhaust manifold WILL NOT fit without some cutting. You can see on the left side of the pic where the curve of the bracket is still interfering with the pipe. That whole lip has to go.

It should look like this, but most likely a bit neater than my hack job:


The intake and exhaust manifolds will bolt up in a similar fashion to the 258 manifolds, though there's no EGR tube to fumble with.



After bolting up the manifolds, install the fuel injectors/rail, injectors to rail first, then rail to manifold. Then install the throttlebody. I bored mine out from 56mm at the bottom to 60mm straight through, and beveled the top 1/2" to mate up with the rubber coupler so there is a perfectly smooth transition from coupler to throttlebody, this adds a lot of response and helps create a venturi effect.




This part will require that you have a welder or someone that does, there really isn't a way around this....
It's time for the exhaust work. Get your 2.25" j-bend mandrel bend pipe, 02 sensor bung, and 2.5 to 2.25 exhaust flare ready. Also, grab that 4.0 exhaust header-to-cat pipe from earlier.
Cut just underneath the coupler flange on the XJ pipe. You'll need this flange. Before you start putting everything together, make sure this goes behind the 2.5" flare. You will need to do much of this by eye, there really isn't a clear way for me to explain it in words, just pictures. I can tell you it will be a VERY tight fit, but it WILL work. The easiest way is to curve the pipe slightly away from the block after it comes off the header outlet, then around the left side of the front driveshaft, then back under it, to under bellhousing, then a 90 deg bend to the trans mount. Mount the cat just after the trans mount, then use a 45deg bend after that, to follow your stock exhaust path, and another at the other end, and have it follow along under the drive's side of the car over the rear axle. Weld on the street hookup flanges to the pipe after the second 45, then install your cat, run the pipe over the axle, then install the cherrybomb.

Though, the muffler has since been switched for a cherrybomb Cheesy


02 bung.



The opposite end from the flange on this section stops right at the middle underneath the bell housing

You can get an idea of the shape here.


VERY tight fit. Remember though, your front driveshaft won't do any moving around, so for as long as it's not against it, the only thing you have to worry about is the front yoke hitting the 02 sensor. In retrospect, I would have positioned it 180deg around the pipe from where it is now. Camera is turned 90 deg counter clockwise.

View from underneath front diff, block at the top behind the drive shaft.

Remember that cherokee midpipe? link that to the opening of your pipe under the bellhousing, putting the cat just behind the mount. Then run your two 45 deg bends, making sure there is at least an inch underneath the driveshaft, it shouldn't be any further out from the t-case than just a few inches or you will run into clearance problems when the rear end is unloaded (big bumps).  After the 45, add your flange to one end, then to the other half to the other half of your exhaust. Remember your pipe over axle clearance will have to be the same as clearance between your axle and bump stop located on the subframe.




Now we can take care of some of the smaller stuff.
The starter wiring, as stated earlier, is fairly straightforward. The heavy gauge red wire goes directly to the positive side of the battery or starter solenoid, and the smaller green/black wire goes to the other side of the starter solenoid. MAKE SURE there is no voltage at any time going to any of the wires hooked to the negative side of the starter solenoid, as this will feed the starter and cause it to remain engaged after the engine has been turned on. Your red alternator charge wire can be hooked directly to the side of the PDC (relay box), where the other large red cable is attached. The PDC should also be wired directly to the positive side of the battery, hence the Scosche terminal, as you'll be using three heavy wires to one side.

You will need that alternator diode mentioned in the parts list, for your field wire, which should be orange with white stripe, in most cases.
Crimp the red end facing toward the alternator, and the blue away from it. This keeps voltage from leaking back into the system after the key has been turned off, so the engine will shut off as it should.
Here, you can see it wired in, along with placement of the ignition coil:


If you have not done so already, install your high flow thermostat, making sure you have the two wire temp sensor on the housing. The 258 thermostat housing cannot be used, though it and the 4.0 share the same t-stat. The temp rating should ONLY be 195 degrees, no more, no less. The computer depends on the engine maintaining this temperature for proper tuning. If your cooling system is in good shape, a high flow thermostat and some good anti-freeze is all you'll need to keep the temps down, even with towing.

We will get to the distributor in a bit, as there is an easy way to clock it, and it's not quite essential, yet. Your starter and ignition system needs to be wired up first.

We can go ahead and install the fuel system components as well, such as the pump, filter, regulator and lines. Mine is a returnless style system based loosely on the 4.0 Grand Cherokee system.
The fuel pump should be installed as close to the tank as possible, and as low as possible, but keep in mind what other parts may come in contact with it at extreme suspension articulation or heavy mudding/offroading. I installed mine like this:

I used two 2" conduit hold down brackets from the hardware store, and some spare insulation from a previous parts vehicle, to insulate the body of the car from pump vibration. The fuel plumbing is fairly easy, simply run the line to the fuel filter, then to a brass tee connected to the regulator, and to the rail from there:  I used a two hole pressure regulator, one in, one out. My line runs from the pump to one side of a tee... the line directly across the tee goes to the fuel rail, and the line coming off the tee goes to the inlet side of the regulator. The outlet side of the regulator is plumbed back to the return port on the fuel tank. Basically, the line between the rail and the pump is pressurized to whatever the regulator is set at, and whatever excess pressure is generated goes through the regulator and exits out, back to the return. All of this is at the back end of the car, close to the tank.

If you choose to use a return rail, forget about the aftermarket regulator, just run your line off the pump to the inlet on the fuel rail, and run the exit line to the metal return line in the engine bay.

In either case, you MUST upgrade your rubber hosing to EFI RATED hose. It cannot be simply fuel/emissions hose, it has to be rated for EFI, otherwise your hose will burst once the pump is primed. Also, double clamp your hose wherever you can. You will need approximately 8-9 feet of hose. Make sure your lines are not going to get caught in any suspension components, or touch any part of the exhaust anywhere. If you mount your pump directly to the spare tire well above your diff, keep the travel of the rear diff and cover in mind.

Now that just about everything under the car is done, it's time for wiring.

First, make sure ALL sensors and equipment are present, that you will be using
-Fuel injectors
-MAP sensor
-Intake air temp sensor (located on intake manifold)
-Crank position sensor
-Cam position sensor/distributor (one in the same, located in the dizzy)
-ignition coil
-2 wire coolant temp sensor (on thermostat housing)
-single wire coolant temp sensor (located on cylinder head at the rear, same place as 258 unit)
-VSS (vehicle speed sensor)
-fuel pump
-Throttle position sensor (on tb)
-Idle speed motor (on tb)
-Oxygen sensor(s)
-knock sensor, if applicable (my harness had no provision for one, nor was it ever mentioned at any point in the FSM)
-AC system, if applicable (mine came without)

The easiest way to go about this is by first removing ALL of your old engine wiring harness and computer. It should disconnect from the chassis harness (not at the firewall) under the hood. You will not be retaining any of your old engine harness other than the coolant temp sensor in the cylinder head, and your oil pressure/level.

Next, drape your new harness over the engine bay, routing it so the large 60 pin connector (should have a bolt going through it) sits about where your washer bottle is, and the PDC sits close to your battery. This is approximately stock location on a Jeep, and since your sensors are in the same locations, it should make it easier. Also, just a note if you're reading through this and have not obtained your harness, DO NOT hack through your harness when you get one. Retain every connector that goes to every sensor mentioned, and then some, or you will create a world of headache for yourself.

Ever connector on the harness should be different. Not by much, but enough that they will connect only to one particular sensor. You may have to locate a fuel injector wiring diagram to make sure your injectors are connected in the proper order, but it's extremely easy to find one and easy to decipher it.
Some connectors are grouped together, such as those around the throttlebody and CPS, along with injectors,2 wire coolant temp sensor and oxygen sensor. Those are amongst the easiest to find, and the first you should connect.
The intake air sensor located on the intake manifold is fairly easy to locate the connector for as well, though if you can't find it, don't worry about it yet, it won't mean the difference between running and not.
From there, connect the three large ground wire group on the other side of the engine to your dipstick bolt, or somewhere close to it, on the engine. This is one of the main grounds for the harness. Your coil and dizzy connectors are located within a foot or two along that set of wire. Again, do not worry about the dizzy yet.
Next, locate your fuel pump wires, coming out of the PDC. There should be two of them, each one green with white stripe, coming out of the bottom of the fuel pump relay bay in the PDC. They're slightly heavier gauge than the other wires in that bay.
You will only need one of them, this is your fuel pump + wire, it goes directly to the terminal on your fuel pump. The other terminal on the pump is ground, and it should be grounded somewhere in the engine bay, on the body of the car, in a clean secure location, with the same gauge wire.
If you have not done so yet, mount your map sensor above the valve cover on your firewall. The plug for it is a three prong, with round terminals, and is green. Don't forget, there is a vacuum port on the sensor that must be connected to manifold vacuum as well.

Your vss wiring is going to be a bit different... It is a two wire sensor, but the XJ harness has a three wire connector for it. You will only need two of those wires to connect it.
With the clip of the connector facing up, the black/light blue (sensor ground) wire connects to the right side of the connector, and the orange/white stripe (signal wire) connects to the left side. The orange 8v supply is not needed because the sensor is a hall effect device that generates its own voltage.

The orange/white stripe and orange wires are common wires for nearly all sensors, or those that need voltage supply, and these wires should not be severed other than to connect the vss.

It is best to wire this up before installing your cluster, as you may have a hard time installing it. You will have to remove some insulation from inside the firewall in order for the sensor to fit, and you will either have to loosen your entire dash and pull it out and down a few inches, or install the sensor/fitting to the back of the speedometer after your cluster is installed. I have not tried the second option yet....

There are three heavy gauge blue wires coming out of the bottom of the PDC
, they should be hot in "run" and start/run. These three wires are all spliced together, so it doesn't really matter which one you cut. YOu can even use one for accessories, as these wires will be hot with the key in run position. Either way, it should connect to your old yellow coil wire, as shown.

Now, if you have wired it properly, it should attempt to kick over when you turn the key. You should hear the fuel pump buzz for 1-2 seconds when you turn the key to run, then it shuts off again. This is the pump priming. Disconnect your coil, and keeping track of all wiring to make sure it's out of the fan blades, turn the key. If the starter kicks over, you're almost there!
Now you can install your distributor. First, remove the #1 spark plug from its cylinder. Tightly wad a paper towel up and stuff it in the spark plug hole. Key the starter juuuuuust barely, as light as you can, until you hear (or see) the wad pop out. As soon as it does, check the piston location in the cylinder, with a 3/8" drive extension, being careful not to touch the cylinder walls with it. The piston top should be close to 1/4" down from the hole. If so, you've found TDC. I've discovered this is the ONLY reliable way to find TDC, as you can hand turn the engine all day and watch the crank damper position all day never get it right.
use a screwdriver to position the oil pump slot in the distributor hole to the 11 o clock position. Locate the #1 cylinder on the distributor cap, and turn the rotor so it faces approximately at #1 on the cap, with the cap in position for installation. Rub some grease or engine oil on the gears before installing, then slide it slowly into the hole. It may catch approx 1/4" before settling completely. If slightly moving the rotor does not fix this, pull it back out, and either turn the rotor slightly or VERY slightly turn the oil pump slot. The gears and slot have to mesh properly. Compare with the cap, making sure the rotor points at approximately #1. If so, remove the distributor, and cut the ears off the right side of it. You will want to mount it as such that the bolt mount hole would have been covered by the ear closest to the block, and tighten it down. Technically, these distributors are NOT adjustable, however you can bend that rule if you create an adjustable crank sensor by slotting out the holes. However, unless you run E85, you shouldn't worry.

Now reconnect the coil, install your plugs and make sure they're at the right firing order, which is the same as the 258's, 1 5 3 6 2 4. Make sure all connections are tight, all vacuum lines have a destination or are plugged, and make sure there is no fuel leaking.

If you had not previously filled your driveline and engine with fluids, do so now.
 
Then, the moment of truth. It should start right up Cheesy If it does, don't touch the throttle, let it sit and idle for a few minutes, so the engine computer can get used to the injectors and engine size. If it cranks but no start, check for spark at the coil. One wire should be putting out twelve volts to the coil, the other should be putting out 5. There should be no ground wire tied into the coil connector (that was my mistake, fixed it and it started right up).

If for any reason you cannot get it to start, break out your multimeter (not just wire tester, it needs to have a volt meter, and continuity tester), and start testing all circuits for voltage. If you still can't figure it out, let me know and I can help you work through it, my harness was completely butchered and I had to piece it together in places most of you won't have to, so I got to know it quite well.

A footnote: I would advise you to hook up a check engine light. With an OBD fuel injection system, that light becomes important, as it can indicate a major sensor malfunction, which can result in driveability problems. You WILL have two codes that will always be present in the computer (and cause a light): Fan relay circuit fault and alternator generator field fault. The first is fixed by converting to an electric fan and wiring it directly into the fan relay in the pdc, instead of using a standalone relay. The second is remedied by converting to a 4.0 alternator. The AMC alternator runs all the time, the 4.0 alternator is computer controlled, and turns on when needed.

And lastly...
I want to thank the following:
Everyone here at the Nest. Your support and help got me through the mess, and helped me work through all the rough spots, getting my car to where it is today!
Everyone at Jeepforum.com, even though not a single question I asked was ever responded to, the responses to other posts were critical in helping me figure out some of the wiring, especially the VSS.
Everyone, especially Jeep-Power, at Jeepstrokers.com. YOU ROCK!
Dino savva, @ jeepforum.com, for your extremely informative site on strokers, which included all the information one would need to know about stock 4.0 specs.
Bennie, @ Hesco, for your advice and help with the fuel pump and fuel system layout.