Can you get a picture of the problem area please. I extend, modify etc harnesses all the time and no one would ever know that I've been there except for some clean black tape on the loom. If things are running properly, why change the whole harness unless something is seriously wrong, you can make it look factory clean for a lot less effort.
I'd go with a 99 harness if that's what you car is... then have your pcm programmed to the right stuff as a 99 instead of a 2001 and put the right vin on it.
