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 build #48. Bolt ons, suspension, Novi 2000.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.