From Experience.
I removed a 95 3.8 and replaced it with a 02 3.8. I tore down both wire harness' and then made a custom out of the 2 so I could put it back inside the 95 and still use the same computer I have always had.
If there is a kit that makes this easier, you should consider using it. If there is not a kit. The first thing you need to do is get a manual for both engines. In my case its the same manual. That way you can check out all of the wiring and make things work correctly in the right pin so its compatible with the computer that you will end up using. If you do tear into both harnesses like I did. The one you need to use will be the one that is coming out of the car that you are putting the new engine into. This is because the pins at the block on the firewall will match up correctly and you only will have to worry about what is from that point to the end of the pigtail in making the wires functional. In my case I needed to use sensors and things from the 95 on the 02 so the computer would stay happy. In that I needed to use pigtails off the 95 also to make the senor happy.
Its a matter of choice, in my case the custom route was the only option.