Alright so I tried posting this in the "Mopar V8 YJ Owners" group, and apparently you're only allowed to post 1000 characters at a time. Since I don't know where else to put this, I'm posting it here in YJ Tech since this is intended to be specific to YJs. I'll let a mod decide where it needs to be properly placed.
Be forewarned that some of the information below might need to be corrected, I intend to correct it as people inform me of the errors.
This is intended to be a basic guide to those who have questions about this swap. The questions that are most commonly asked about this particular project are answered here. Lately there has been an increasing amount of interest in the 5.2 and 5.9 Magnum engines for YJs (and TJs as well), so the need for a how to guide, or reference guide is growing.
Any false information that needs to be removed, or information that need to be added, or corrected will be done so once I am notified. I am relying on those who are knowledgeable about this swap, and those who are knowledgeable about the parts listed here to help me in making any corrections that need to be done.
Some would agree that if you're starting with a YJ that has the 4.0 and AX15, you're ahead of the curve in some areas. The AX15 is a common transmission used in the 5.2 swap. The AX15 has also been used behind the 5.9 in a few cases, some with success, others unknown on whether or not it has held up. Some results for the 5.2 and AX15 have been less than satisfactory, while many haven't had any problems. The biggest factor in it is how you drive. If you are relatively conservative on the throttle, the AX15 is perfectly capable for the job. If you like to do 4WD burnouts at any given opportunity, the AX15 might not last very long. If you do decide to use the AX15 behind the 5.2 or 5.9, you will need to remove the stock bellhousing on the transmission, and replace it with one from a mid to late 90s Dodge Dakota that had the 3.9L V6, if you desire an external slave cylinder setup (which is recommended). That bellhousing, when attached to the AX15, will allow the transmission to bolt up to the 5.2 and 5.9 without any adapters. The Dakota 3.9 bellhousing is relatively easy to find.
The AX5 that came behind the 2.5L engine is notorious for failing even behind the 4 cylinder. It has a reputation for being an extremely weak transmission, and should not even be looked at for a a V8 drivetrain.
The NV3500 that came in the Dodge Dakota and Dodge Ram came behind the 5.2 from the factory. It bolts right up to the back of the engine without any need for adaptation. The NV3550 is simply a later version of the 3500 that has a removable bellhousing.
In order to use the NV4500 behind the 5.2 or 5.9, you will need to find an NV4500 out of a Dodge Ram 2500 with the 5.9 gasoline engine... not the 5.9L 6 cylinder Cummins diesel. It would be a 90s model Dodge Ram if that is the route you were to choose.
For the NV3500/NV3550 or AX15 transmissions, the clutch kit will need to be for a 90s model Dodge Ram.
Clutch and Flywheel
The 5.2 and 5.9 are balanced differently, the 5.2 is balanced internally, and the 5.9 is external. What that means is the flywheels are different so use the correct one for the engine. When using a manual transmission behind a 5.2, you'll want to use a flywheel from a 90s model Ram 1500. When using a 5.9, 90s model Ram 2500.
For clutch kits, if you're using an AX15 from a YJ or TJ, you can use the pilot bearing that comes with the clutch kit, the OD of the pilot shaft needs to be .750" for it to work. If you are using an AX15 from a different vehicle, you'll need to do some handy work with the pilot bearing.
mike_breaker_5 explains in post #37
Do not use the stock I4 or I6 clutch with this swap, it will not work, and if you make it work, it still won't work.
If you're using a 5.9 with the AX15, a 5.9 clutch will fit inside the AX15 bellhousing perfectly fine.
Torqueflite 727 aka 36RH/37RH
The 727 transmission is an aluminum case 3 speed automatic, that was manufactured from 1962 to 1994 in various AMC and Chrysler vehicles. It has a long reputation for being an extremely stout transmission, both in the off road world, and the muscle car world.
For AMC vehicles, the 727 came in the AMC CJ7 and Grand Wagoneer. It was also used in other vehicles that had the AMC 304, and 360 engines. Information on being able to convert a 2WD 727 to a 4WD transmission is yet to be found. That information will be updated as it is found or reported.
The 727 bolts up to both the D300 and NP231 transfer cases without adaptation. However, due to the clocking of the transfer case, you may or may not experience clearance issues with the drive shaft and skid plate in a YJ.
This section will be updated as more and more people start to use automatic transmissions with this swap. Not enough people have done this swap with the automatic transmissions that came behind these engines. The lack of information on the bugs or problems that need to be addressed for this swap is too much to make any statements. The most well known issue so far, at this time, is the drivetrain length being too long.
The NP231 is the most common transfer case used in this swap, and it bolts up without adaptation to most, if not all of the manual transmissions listed.
The D300 transfer case is a sought after upgrade that requires an adapter kit, and needs to be flipped if it is being used with driver side drop axles, or the stock front axle.
More transfer cases will be added to the list as people utilize different ones, and information on them becomes more available.
Novak and Advanced Adapters make engine mounts for this specific swap. The 5.2 and 5.9 Magnum engines have the exact same mounting points and locations, since the blocks are the same. What that means is, if you swap in a 5.2 and later on decide you want to bump up to a 5.9, the 5.9 will simply bolt right in to the motor mounts you installed for the 5.2 without any issues.
There are many choices out there for the PCM (computer) for these engines. For the 5.2, the vehicles that have the proper computer would be the ZJ Grand Cherokee, Dodge Ram, Dodge Dakota, Dodge Ram Van, and a few more, but the vehicles mentioned are the easiest ones to source a computer from.
Because of the intended purpose of the vehicles mentioned, they have different fuel maps, but one does not outperform the others. They are simply factory tunes for where the torque and horsepower is concentrated.
If you want to utilize a manual transmission, it is best to find a computer from a Dodge Ram or Dakota that had the 5.2 or 5.9 with a manual transmission. The PCMs that came with the automatic transmissions can be used as well, but you have to bypass the Neutral Safety Switch in order for it to work.
One question that has been asked many times before in various build threads for this swap, is security programs written into the PCM. Dodge Ram and Dakota PCMs don't have one, however ZJs and Durangos do. So if you're using a PCM out of a ZJ or Durango, be advised. That'll be an issue you'll have to address before you can start the vehicle.
EDIT: Apparently some of the PCMs (for the 5.9 at least) will have a two plug port, and some will only be a single plug. Make sure you do your homework if you're buying parts separately. If you're getting all your parts from a single donor vehicle, chances are you won't have anything to worry about. If you're swapping a 5.2, you might want to do the same homework in case the PCMs have the same situation.
EDIT: OBDI computers have 3 plugs, and OBDII have a single plug.
Having the wiring harness that was attached to the engine would be a big plus, but if you do not have it, any wiring harness for a 5.2 or 5.9 that isn't cut or hacked up will do just fine. You need the ENGINE wiring harness. You splice that harness into your factory harness and you use the PCM from the donor vehicle with your now modified harness. All of the Chrysler PCMs from the mentioned donor vehicles are the exact same computer as the stock PCM in your YJ, same ports, same shape, they just have a different program written in them.
One of the benefits of this swap is that the donor computer speaks the same language as your stock gauges, so they communicate perfectly. You have no need to go out and buy aftermarket gauges with this swap.
For the CPS, the manual and automatic sensors are different. The automatic CPS is longer and will make contact with the tone ring on the flywheel if you use it with a manual flywheel. You can use washers as spacers for the automatic sensor.
With a little craftsmanship, you can use the stock 4.0L radiator with the 5.2 and 5.9 engines. Based on the information available at this moment in time, the stock 4.0 radiator does fine cooling both engines. It does however require some craftsmanship with the radiator house routing.
Those who go with an aftermarket radiator should look for a radiator made either specifically for a Chrysler small block conversion, or a Chevy conversion radiator since the inlet and outlet are on the same sides.
Aluminum radiators are almost always, if not always, recommended when going to an aftermarket radiator. As to the amount of cores and rows, that is up to the owner to decide. Electric fans are also ideal.
The stock 5.2 and 5.9 exhaust manifolds will not allow proper routing of the exhaust, except for a couple vehicles [information on what vehicles is yet to be gathered]. The best, and most common solution are aftermarket block hugger shorty headers. Long tube headers will not work with this swap, and neither will a true dual exhaust. You are simply stuck with a short tube header, Y pipe, single out exhaust setup if you desire long tubes with true duals.
A more advanced, in-depth guide including part numbers and common issues during the process of the swap will soon follow.