Well if it's like most harness/engine swaps it will probably be a little bit different between the two. Just the fact that it's a different year and efi setup entirely pretty well guarantees there will be differences.  Can it be done though? Definitely.
The best bet would be to find the most accurate electrical schematics and wiring diagrams you can get. Factory manual in other words.
As far as what will be different, you'll probably have to do a little bit of splicing on it just about everywhere.  Just off the top of my head, the differences between the 4 door and 2 door portions of the vehicle aft of the dash will be a little different.  Connectors could be a little bit different between the harnesses being as it's different model years. ÂÂ
The trim variations between a Tracker and Kick could be a little different too such as the Tracker having a different setup on the brake lights/turn signals since they don't have an amber turn signal so the logic for the lights will be a bit different than on a Kick.  Or just swap in the lights from the kick and use that harness if you can, I personally prefer amber turn signals since they're more noticable.
Dashboard forward I would suspect that you will replace almost everything  since the 16v is completely different being a port injected engine instead of a TBI like on the 8v.
It's a pain in the butt job no doubt about it, get a good volt-ohmmeter just for stuff like checking continuity and things like that. If you havent' got factory manuals you'll probably wish you did, they tend to be a bit better and updated for errors compared to a haynes book.
Depending where your 4 door is damaged from rolling you might have to completely replace a few sections of the 16v harness if you can't get them out because of the metal around them being mangled or if they're damaged.  You may have to swap some of the guage clusters etc but I'm not sure since I've never dealt with the 16v/4 door models.
Also make sure you keep in mind stuff like the crossmembers for the tranny/t-case since it may be a bit different.
Overall it's not usually too rough it's just the little details that usually cause the bigger headaches when you do these.
Honestly, if it's possible, the easiest way to do this would be to completely remove the 2 door harnesses and use everything from the 4 door. Just remove stuff like the door switches for the dome light for the rear doors and stuff like that. You won't have the rear defrost to worry about but it's normally off so that's no big deal. Stuff like that you can just leave disconnected and honestly you'll probably get it done a whole lot quicker if you go that route.
