2.5l to 4.0l swap

I have a really clean 1996 cherokee that has a 2.5l and 5 speed. I know most guys say sell it and buy one with the 4.0 but rust free cherokees are pretty rare in Wisconsin. Plus mine has the 4:10 axles already. I have a 99 4.0 with a wiring harness from an xj with an auto tranny. I am rebuilding an ax15 and plan to swap the motor in this summer. I have a few questions for anyone who has done this swap.
Will the wiring harness from the 99 with an auto tranny work in my 96 with a 5 speed? Or am I better off trying to find a wiring harness from a manual jeep? Any other tips would be appreciated!

It'll take a lot of work to get the 97/98+ wiring harness to work with the 96- dash wiring and IP... probably not worth it. If you can find a 96 4.0 wiring harness (engine and engine bay plus computer only, don't need the dash or interior) you can use the 99 4.0 just fine iirc, might need a sensor or two swapped but no big deal. Don't need to worry about auto vs manual computers on a 96, worst case just leave the TCU under the dash and the harness plug for the AW4 dangling then bypass the NSS.

I definitely agree on keeping it, a rust free clean body is about all I look for in an XJ now. The rest is bolt on junk you can scrounge from junkyards, buddies, and craigslist...

Cool. Is the 96 wiring harness similar to any other years? I talked to my dad and he said the guy he got it from pulled it from a grand cherokee and had it in a 95xj and the harness I have is from a 95.. I'm going to a local yard with a bunch of cherokees in a few days...

95 is probably way different, many sensor connectors changed over from 95 to 96 for the OBD II switch. 97 is also way different unfortunately... due to continued changes and upgrades. 96s are really a bastard stepchild electrically in many ways. Fortunately they made 280k of them, I can usually find 2 or 3 in the local you pull it on any given day.