I have a 99 XJ with a lot of mods done runs super strong, problem is rust. Starting to lose frame, rockers are toast and floor is starting (was a Northern PA jeep lots of salt). I love my jeep and want to take engine, trans etc and swap into another XJ shell. From what I have searched it looks like for easiest swap find a 96 to 99 correct? I would rather not swap the harness if I don't have to. If I could find a 2 door sweet. Can anyone lend some advice I have searched and still not a 100% on what to do. Thanks

Why not? probably the easiest part of the whole thing.

What years can I swap all my powertrain in and harness into? Would I have to use my dash or could use any?

If you are looking for a direct one-to one swap...
98-99
97 is a b*st*rd-child with far too many wiring differences and a few subtle mechanical differences that it will be a real bear to work with. I've got a 97 so I'm very familiar with them.

In addition to what SeriousOffroad said; in '98 an additional transmission speed sensor was introduced (which carried through to '01). If you went with a pre-98 body you would need a '98+ wiring harness, PCM, and TCM inorder to run your '99 transmission.

Edit: Forgot to mention that in '99 the fuel injectors were changed and they used EV6/USCAR injector connectors. Previous years used EV1 connectors. So, if you pick a '98 Xj to do the swap, you'll need to change the injector harness over from your '99.

I have been trying to find a engine for my 99 and found out only another 99 will exchange unless you do a lot of changes wiring, mounting brackets to block etc. But if you have the complete Cherokee it came from it may not be as big an issue.

Fred