Welcome to the wonderful wonderful world of buying a used modded foxbody. Dude probably didn't want to have to have the key in to work the windows and went nuts with some butt splices. I'd see about getting a new harness and replacing the whole thing if you plan to keep the car.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.