I really hope the 4.0 is worth all this work, just by pure numbers it kills the 2.9 in torque, can't wait to drive it and I'm curious what my fuel mialge will do since I drove my 2.9 like a rented mule to make it go anywhere (I seriously was super hard on it the last year or so, amazing I got the milage I did), never thought I'd actually do an engine swap other than using another 2.9 but really, the wiring isn't bad at all if you can read the diagrams. So officially now none of my original drivetrain is in left in my rig except the rear carrier, before the 4.0 swap only my engine was the only thing I hadn't swapped. If you ever do a 4.0 swap, deffinatly get a running donor, I'd hate to have to hunt down all these little random parts. I've got somewhere around $350 in my swap including the tranny, and I've sold hardly anything of the donor splodor yet, also my old tranny is for sale so that will help too.
EDIT: Thanks Dishtowel!
Gremlins shouldn't show up, all but a couple wires that I'm splicing and adding length to are being done with the same color coded wire taken from the power distribution and 2.9 harness for easy tracing in the event something does show up.