What ended up being the problem with the 4.0 swap?
Just curious as I did a 4.0 in my '7 and am always collecting info for reference.
So as far as you can tell just the fouled injectors...not too bad. They always run rough until the PCM has a chance to re-learn. I'm on a CJ only forum where they have some 4.0 swap guru's if you run into problems in the future. I can fo-sho feel your pain with the wiring part here's what mine looked like.
Took a little longer to find these as my oldest daughter decided to "organize" the picture folder on my laptop. But anyway here's what my 4.0 swap started with.
http://i246.photobucket.com/albums/gg114/jimijam19K/40wiremess_1.jpg[/IG]
[IMG]http://i246.photobucket.com/albums/gg114/jimijam19K/40wiremess_2.jpg
It's been up and running for a couple years now, maybe i just worded wrong. I've run three different transmissions so far (T5, 999, 727) and am thinking of changing again. Biggest reason I used the CPS relocation from Hesco, didn't want to redo a bellhousing everytime I switched trannys.
BTW I think I remember seeing that CJ when it was for sale on CL, did the PO live down'round Chehalis/Centralia somewhere?