I can chime in here too. 97-02 use a 100 way connector above where your left knee would be. This is where all of the vehicle wiring “integrates” and is sent it’s separate ways. They changed that to a totally different style in 03 that makes it much harder to swap things.
In addition, 97-00 is CCD bus whereas 01-06 is PCI bus, so you would have to change gauge clusters. The radio is a different plug, as well as the HVAC controls, which are slide/cable style in 97-98 vs knob style in 99-06.
And speaking of that, you’ll have to convert your HVAC wiring to work with the knob style, otherwise you’ll need to get an HVAC box that works with the slide/cable style. And you’ll need to change out your dash too because the center portion where the radio and HVAC controls go is shaped different behind the bezel where it sits up against the HVAC box.
Like Chris said above, your best bet to make this work with your donor is to rip EVERY wiring harness off of the donor and put it in your 03. Engine, PDC, dash, and your rear wiring which is integrated with your fuse box harness too.
Unfortunately this is far from a plug and play swap. Even though the 4.0 is a Jeep engine, you’re essentially trying to swap in an engine that your specific Wrangler wasn’t designed for. It’s the same concept as trying to swap out the 4 cylinder motor in a Honda Accord for a V6 Honda motor which DID come in certain Accords. Eventually you could get all of the electronics to blend but it wouldn’t be an easy task.