Before I did my swap, info was spread over a bunch of threads. I will try to include as many details as I can. I didn't take many pictures during, but I can grab a couple as requested.
Started as a 1994 with a 2.5, ax5, and an np231 with a frame that I tried to patch in 4 places. My transfer case was wasted, and my ax5 was on its way out, and the 2.5 was leaking more oil than I could put in it.
I bought a complete 4.0, ax15, np231 drivetrain from a 1994 cherokee, with the engine harness and computer. I took it home to tear it down, cleaned the head, lapped the valves, and left the spotless bottom end alone. Got myself ready to drop it in. Cut the mounts off of the 4 cylinder frame, and while I was under the jeep trying to align the tcase, I noticed holes in the crossmember in front of the gas tank. That was when I decided to find a 6 cylinder frame.
In the meantime, I found a SYE kit and a driveshaft, so I ended up rebuilding the cherokee tcase and adding a SYE. I was curious as to why I broke the case on my old transfer case, my shift fork was pretty worn I guess and there was more metal than fluid. One other thing I found was that the Cherokee tcase is clocked down further than the wrangler, and the tcases are the same. I had planned on using the front half of the wrangler tcase, because I thought that was where the clocking was adjusted, this is wrong. The holes on the transmission flange are where the tcase is clocked, so I measured what I needed and my machinist dad made a jig for me to drill holes clocked correctly, 12 degrees clockwise.
Finally found a frame, unbolt and rebuild was pretty straight forward and I must say I am much happier and sound minded that I have the correct, solid frame for the drivetrain, but this may not be an option for many but this seems like the best way to go.
Wiring the motor was much easier than I thought it would be, I used the 4 cylinder engine harness and spliced in two injector wires into the original bulkhead connector for the ECU. The pins are 38 and 58, for cylinders 5 and 6 respectively. I grounded the new injectors into the existing injector ground wires. Everything else was plug and play, plugged the cherokee computer into the bulkhead, all the sensors plugged in, I just had to extend a few wires to the coil, oil pressure sending unit, and maybe a few more, but its pretty clear which wires are too short. I had to extend the fuel lines as well, I used 5/16" rubber fuel line and hose clamps. All of my 4 cylinder accessories bolted to the 4 liter, power steering pump, alternator and alternator brackets, and I used the wrangler 4.0 water pump so I could reuse my 4 cylinder fan and fan clutch.
Now that its done and running again, I'm definitely impressed with the difference in power compared to the 4 cylinder, but there's definitely some kinks to work out. As of now, I'm not running a fan shroud, it runs at 210 on the road, but in the woods or mud when there's not alot of airflow, it runs pretty hot (260ish degrees) even with a 180 thermostat in it. I also used the 4 cylinder front pipe for the exhaust, its angled wrong for the 4.0 and I had to hack it up to make it work. I hope this helps clarify some problems, I know I spent countless hours crawling the forum and found a ton of sporadic, contradicting information. Keep on Jeepin' on