Luke- I was just about to post this info - here I'm going to guess you've got one harness that may not mate up and one that's extra? Its for some wierdo emissions stuff, this is what I figured out for my swap project maybe it might help?
http://www.chrisstorer.com/turbo
Theres a htm file with some wire colors and what they do.
May want to pick up a haynes book - its the only thing thats good for lol.... even my 2 FSM's (for a 98 200 my sis has now and my 97 fsm don't have wiring diagrams like haynes)
Best of luck luke.
Chris