Trying to get it mostly right the first time: A 5.9 Magnum and 46RE swapped, Tummy Tucked Daily Driven Jeep TJ

Wiring Part 1 – The Approach

The wiring for this swap seems to be what scares people the most. The intention of this post is to provide a guide for how to pick up the FSM from both your donor and your TJ and work through this swap.

My search for a donor started with confirming which vehicles would be compatible with the TJ's CCD Bus setup. Break out the Google machine if you're unfamiliar with that as there is a ton of information online that I won't get into here. I wasn't terribly picky on what my donor rig was, so I bought what I could get cheap and around here that's Durangos. I also have a but of a soft spot for the GCs and would hate to cut one up. So far I haven't found anything that makes a Durango (and I'll loop Rams and Dakotas in here too) substantially better or worse than a Grand Cherokee. I'll touch on those differences later once I've confirmed what works from the Dodge.

Remember, I am going from a 1997 2.5L AX-5 to a 1999 5.9L 46RE out of a Durango. Everything engine related would apply if I kept a manual transmission, but since I am swapping an automatic transmission in place of a manual, I elected to use the Dodge engine harness and make it 'plug in' to the Jeep harness. There are too many circuits related to the automatic transmission I'd need to add to the TJ harness for it to make sense as the base.
Both the Dodge and Jeep have 3 plugs on the PCM; 1 is a body harness and the other 2 are engine related. Additionally, there are 2 plugs that tie into the PDC to provide power and grounds (C103 and C104 on the TJ and C105 and C106 on the Dodge). This means that you can separate the 'engine' harness from the rest of the wiring harness. The PDC plugs for both the Dodge(C105/C106) and the TJ (C103/C104) have many of the same circuits in them but utilize different plugs which prevents this from being a re-pin, plug and play deal.

Now, let's talk about the splicing / de-pinning that many other threads mention. Splices are fine when done correctly, but that's a pretty tedious process. Add to that the factory connectors are over 20 years old and very brittle, so de-pinning them would likely end up with a broken connector. And I'd probably end up with the pin tool stuck through my hand.

To avoid all of that, my goal is to cut the plugs off the factory harnesses and swap to a common Deutch/Molex/ Delphi type plug where I can match the pins to their prospective circuits, plug it in and go. As mentioned before, I didn't want my TJ down for a long time during the swap, so I purchased a 97 TJ 2.5/AX-5 engine bay harness, including the PDC, off eBay for about $150. I bought. It occurred to me later that since I'm swapping to an automatic, it might have made more sense to purchase an automatic TJ harness since the control relay would already be there. Even if you don't buy a spare harness, I'd strongly recommend unplugging your TJ harness and laying it out on a table.

It took me a minute to figure out where to get information in the FSM. THIS thread and THIS thread were beneficial to read through. Here's what I learned:
• Since all the changes were being made at the C103/C104 and C105/106 plugs, and many of these are fed from the PCM, I started looking at the PCM circuit descriptions under the Connector Pin Out section. I built a simple Excel spreadsheet that listed the cavity number, circuit number, wire color and size, and page number. This Excel sheet has been major asset for the electrical portion of this project. A link to it can be found HERE.

• Review the rest of the Connector Pin Out Section and fill in the remainder of the circuits. Be sure to note what plug it appears on and page number in case its needed for future reference.

• Compare the TJ C103/C104 to the Dodge C105/106 and make notes of what matches. I used the spreadsheet to create pinout guide by copying and pasting. The neat thing about this swap is that many circuits use the same (or similar) wire colors, gauges and descriptions.

Here is a sample of the spreadsheet I created:


Part 2 will get into the actual execution of this plan.

I have completed the wiring on the body side of the harness and have the rough shape of the engine harness completed. I'm waiting to trim wires down to length until the motor is in the TJ so I don't cut anything short. I've also started tearing the motor down to re-paint it, install the Hughes plenum plate and see what accessories, sensors, etc might need replacing while I'm here.

Getting the engine in my shop was a little bit of an adventure. It started with getting the motor off the trailer with the help of my Jeep co-dog Mitchell. He's a rescue that found us at Lake Mitchell (hence the name) when he was a 6 week old puppy and we couldn't stand to leave him. After 2 years I'm not sure who has trained who.





I then had to build a new ramp since my old one was a loaner from work and wasn't tall enough. Since I have gravel around my shop, I had to drag the motor up to the ramp with the new multi mount winch I built from leftover Rhino parts. To get it into the shop I lagged a D ring to a joist in the floor, rigged up my snatch block and started pulling.



The end result:



With the motor torn down and an initial parts list ready to order, I'm bringing the 98 TJ home this Saturday to start mocking up the swap and see what else I might need to order in addition to the motor parts. The big ticket items I want to verify are:
• Will the stock Durango exhaust manifolds and y pipe fit the TJ?
• Inspect the transmission to see if it needs to be rebuilt.

My goal is to hear this run by April 1st. Here goes nothing.

That might be the most interesting way to get a motor into a shop!

Couldn't just back the trailer up to the shop door?

xjcrawler said:

Couldn't just back the trailer up to the shop door?

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I didn't have enough room to back the 20ft trailer up to the door without hitting my fence across the driveway. This was far more entertaining anyway.

I'm currently doing the mangnum swap in a LJ got a running a driving grand Cherokee. Issue I'm having is the LJ will start and run for 5-10 sec and then shut down. I think the ASD is active and the Jeep thinks it's stolen. Any thoughts

Dilly_willy_35 said:

I'm currently doing the mangnum swap in a LJ got a running a driving grand Cherokee. Issue I'm having is the LJ will start and run for 5-10 sec and then shut down. I think the ASD is active and the Jeep thinks it's stolen. Any thoughts

Click to expand...

Get an ECU without it.
Also, it should be 3 sec IIRC. 10 seconds is a long time running and that means the anti-theft isn't likely the issue.

Found a individual in my area with a hp tuner and had him deactivate the ASD security mode. Jeep thought it was in theft mode. Fired right up and runs great. Literally every forum I've read everyone says they jus put the motor trans and computer and harness in and it fired right up. Next step Gotta figure out how to get the lj gauges to work. But other then that drives good

Dilly_willy_35 said:

Found a individual in my area with a hp tuner and had him deactivate the ASD security mode. Jeep thought it was in theft mode. Fired right up and runs great. Literally every forum I've read everyone says they jus put the motor trans and computer and harness in and it fired right up. Next step Gotta figure out how to get the lj gauges to work. But other then that drives good

Click to expand...

Good deal. That's typically the issue when it will run and then shut right back down.

What year was your donor? Assuming it was a ZJ, consult the google machine on CCD vs PCI Bus. I'm far from knowledgeable on that topic, but I have run across a thread that went into detail about the differences and how to make one talk to the other.

I finally have something that gives the resemblance of progress!



Since Alabama weather in March is a mixed bag, I've tried to have stuff to do both in my shop and outside so I can maintain progress no matter the weather. With a BEAUTIFIL weekend of weather forecast, I enlisted the help of my dad to help me drag the green TJ out of storage on March 3rd​ (remember, I want to hear this run on the weekend around April 1st​.)








Side note – I have a few Badlands winches from HF and bought their Apex wireless controller so it can be used on multiple winches. I've had really good luck with the winches and absolutely love the remote. It was used heavily this weekend.



If you recall, the green TJ had a 5.2/44re/231 out of a GC sitting in it, so the first order of business was to pull that out.



Since my 5.9 was in my shop getting a refresh, I opted to use the 5.2 as a mock up. I swapped the 46re transmission and the Durango exhaust manifolds onto the 5.2 to duplicate the final product. I'd thrown the 3in body lift that my TJ came with into the parts bin a few years ago thinking I might use it for something later (I'm kind of a parts hoarder). The body lift was brought out of retirement, cut down to 1.25" and installed to replicate what I have on my 97 TJ.


My wife says I can't ever live somewhere with an HOA. I can't quite figure out why...



The Advance Adapter mounts are (allegedly) designed to work with a 5.2/5.9 and an automatic transmission, so I set them in their recommended place and tacked them in. Using a digital angle finder, the mounts were angled back 5* relative to the flat frame section under the tub and tack welded into place. I researched several tummy tuck threads and most all of the builds required some form of MML. Since a Magnum swapped TT wasn't very well documented, I assumed there was the likelihood I would need a MML, so I opted to keep the AA engine mounts in their recommended location and build some spacers should the engine need any vertical adjustment. Using the frame as a reference again, the engine is currently angled back just shy of 4*, so I currently don't plan to add any spacers.





I raised the transfer case up within a 3/4" of the tub to give myself some room for the drivetrain to move. That tab contacting the body will go away with the SYE.



Up to this point I had intentionally not ordered any headers in hopes that the Durango manifolds and Y pipe fit as-is, mostly for the sake of the time it would save. Much to my satisfaction, everything fit like a glove. Score!





Just take my word that the Y pipe fits. It didn't photograph very well when its all right in your face.

I bolted the Summit radiator onto the grill to verify fitment with the GC fan. It clears the radiator by ¾". I plan to run electric fans, but still wanted to keep the option to go mechanical.

With the engine on the mounts, the transmission / transfer case sitting roughly in their final home, and the manifolds and Y pipe installed I grabbed a cold beer and studied for a bit. Here were my initial observations:

• The Durango manifolds and Y pipe fit well, but wouldn't allow the engine to come back any further if needed. Not sure why it would need to though.
• Just by eyeballing the transmission mount in relation to the center skid plate bolt, it looks like the 46re mount would sit back down in the factory skid plate holes (or at most require the Barnes 4wd skid plate)
• A completely flat skid plate is definitely possible, but you'd have to either bolt the transmission to the skid plate or get creative with the crossmember. The distance from the bottom of the frame to the underside of the CV joint on the front driveshaft is your limiting factor here – its about 1.25".
• This swap might be doable without a BL if the AA mounts were moved slightly forward.

This brings us up to Friday March 11th.

@Dan_Goodwin progress is looking good and enjoying the deep dive into a project I didn't even know I wanted to learn about!

I took off work on Friday the 11th​ to spend working on the Jeep. The goal for the day was to get the transmission crossmember completed and start on the exhaust.

I purchased the Barnes 4WD Crossmember Mounting Set to serve as the foundation. Since the TJ frame tapers in and I wanted the bushings to be parallel with each other I used a straight edge on the UCF skid plate to mark and trim the mounting tabs. I am quite a ways from claiming to be proficient at tube bending, so take my building process as a grain of salt. My skid plate has a 1" drop (measured from the mounting flange to the top of the skid), so I cut 2 1" spacers and clamped up my level to use as a straight edge and figure out the bends. The tube had to be directly under or behind the front CV joint for it to clear the drive shaft, so I opted to put it directly under the joint.



After 2 bends and a few trips back and forth to the notcher, this was the final result:



I opted to use the factory transmission mounting plate as part of the crossmember. It's not as elegant as I wanted, but it was simple and worked. I cut and notched 2 short tubes to tie this mount to the crossmember. And no, I didn't weld those huge gaps – the tubes were readjusted after this was taken.



With the crossmember tacked together, the exhaust was the next piece to tackle. The Durango used 2.5" exhaust, and since I was utilizing the Durango manifolds and Y pipe I chose to maintain that size on my Jeep. Had I started from scratch I would have likely done a 3" all the way back.

The addition of the crossmember made routing the exhaust a tight squeeze, but a fairly simple ordeal. I welded on a pair of 3 bolt exhaust flanges from Summit Racing to mate the new exhaust to the Durango Y pipe and ran the new catalytic converter and muffler straight back to the factory exhaust hanger. An O2 sensor bung was added behind the cat to maintain the stock configuration. I'll let an exhaust shop bend a new tailpipe for me once I have this running and driving.


Spoiler alert: I didn't get ALL this done on Saturday. I can't have y'all thinking I work that fast....

Remember the mixed back of weather I talked about? It was mid 70s the day before. The next morning?





I don't like to bounce around on a project, but I can't help the weather. I spent the next 2 days checking items off my to-do list for the 5.9 since I couldn't just toss this motor in the Jeep after all the other work I've done. I decided to do the following:

• Install a Melling oil pump and Felpro oil pan gasket
• Install the Hughes Engines plenum plate kit. PS – this is a really nice and complete kit. Their directions are pretty great too.
• Install a new Melling timing chain set and Felpro gasket.
• Replace all the spark plugs and wires.
• Install a new belt, tensioner, water pump and a ZJ PS pump bracket.

At my wife's request, I ordered new Weathertech mats for the front. Its almost comical how big of a difference new mats make on an interior.





I blinked and my deadline of hearing the Jeep run was here and I was nowhere close to being ready for that. With the mock-up complete enough, I decided it was time to start hustling on the final product. After about 7 hours on Saturday I had a destroyed carport and had managed to sell the 2.5 engine, ECU and air intake.





I spent Sunday getting re-organized and returning the 98 TJ back to storage. I'll focus on getting it sold once the swap is complete. My next goal is to have the motor and transmission in the TJ by 4/11.

At this point I've given up on deadlines and am simply putting in the hours until this is done.

With the 2.5 out, it was time to rinse and repeat and get the drivetrain set in its final home. A Sawzall, grinder and air hammer (sorry neighbors) removed the old engine mounts. I set the mounts to the same 5* angle back I'd mocked them up for, fully welded and painted them.

The engine refresh was completed, so I turned my attention to the transmission and transfer case. The transmission received a new Wix filter and pan gasket, new overdrive housing (I cracked the old one-oops), new torque converter (another oops – I scrapped the old one) and a sending unit mounted in the pan for the Glow Shift gauge. The pan in the 46RE had some clutch material and minor metal flake but not enough to concern me so I'll run this transmission until it needs a rebuild.

Next was to install the JB Conversions SSSYE. Since the AX-5 transmission that comes behind the 2.5L has a 21 spline input and the 46RE has a 23 spline input I needed to swap the input shaft. I bought a pair of lock ring pliers off Amazon [DG1] and went to work. The only difference I found between the NP231D and NP231J was the output shaft and shaft housing, but since I'm swapping in a SYE that is now irrelevant. I opted to keep my Jeep case and swap everything into it.



There's really not much to the NP231, so installing the SYE was a matter of disassembling both cases, swapping parts around and reassembling. I'd read on other threads about folks buying and swapping in an HD chain, 6 gear planetary and input shaft and here is an advantage to buying a Dodge as a donor (not sure if this is applicable to a GC or not) – my Dodge NP231 already had 2 out of the 3 so there's no need to buy anything.

My NP231D had the same 3 pinion planetary, so no upgrade there. The input shaft was removed and installed into the Jeep case.



It did have the wider HD sprocket and chain:



This shows the differences in the input shafts. From Left to Right: JBC, NP231J and NP231D. Look how short the JBC SYE is!



I installed a thin bead of ultra grey RTV to the case halves, torqued everything to spec and bolted the transfer case back up to the transmission.

The transmission was married back to the engine and the entire assembly went into the Jeep for what should be the final time.

Glad you are making progress and skipped the idea of deadlines. Cool to see side by side comparisons of the transfer case innards.

Did I miss you having a doubler in your set up or is the tranny to transfer case adapter really that long?

Lil ugly said:

Did I miss you having a doubler in your set up or is the tranny to transfer case adapter really that long?

Click to expand...

Nope, that whole assembly is that long. The different color is the new O/D housing.

Next was to install the crossmember. If you're using tabs in a double shear setup, here's a tip to allow easier installation after welding. Whether you're installing a heim joint for steering or a harness mount, install an extra washer or some spacer between the tabs prior to welding. This prevents the tabs from pulling together and making your crossmember, seatbelt, etc. nearly impossible to install. Another note if you're using bushings – be careful not to melt your busing when welding.

I bolted the tabs to the crossmember, tacked the mounting tabs in place then pulled the crossmember. The bushings from the Barnes 4wd kit have a 3" mounting width so I cut a piece of scrap tube at 3.125", bolted that between the tabs and grabbed the welder. You could also do this with all-thread.

Truth be told, I never really liked the transmission mount I'd mocked up before and was on the fence about changing it and after feedback from another forum I opted to change it. The drivetrain wants to rotate around the crankshaft, so the transmission needs to be able to rotate around that axis as well. The way I'd previously designed the mount the transmission was essentially fixed and would have likely broken the weld on the mount or cracked the transmission housing.

The factory Dodge transmission bracket centers the TJ rubber mount over the front 2 mounting bolts, moving it away from the crossmember. Unfortunately, it's far enough away that it creates too much of a moment on the crossmember for me to be comfortable with. I decided to build a custom mount out of 3/16" material and a Barnes poly bushing kit and mount. Here was the final result:





The transfer case was 20.25" from the driver side frame rail to the center of the rear output shaft, so I matched that dimension here. I intentionally shifted the bushing to the rear to make the mounting tabs as short as possible. Yet another tech tip for overhead welding – wear some earplugs to avoid getting sparks down your ear. It's really unpleasant.

I had a few hours after work this week to tackle a small project and decided to mount the transmission and power steering cooler. The transmission cooler mount is simply threaded trick tabs welded to the brace behind the grill. The power steering cooler bolts to a 14ga mounting plate welded above the trans cooler.







Next on the to-do list is to finish the exhaust, install the wiring harness and get power to the starter so I can hear the engine fire up, hopefully this weekend.