Hey again, so I got the replacement engine harness, tore the old one out and replaced it.
Got everything wired back up (Pretty darn sure it's all where this supposed to go), went to cold start it and it made this rather awful sound and rumbled *alot*, I shut it off as quite frankly it scared the **** out of me, it usually cold starts just fine and the rumble and whatever that squeak is is definitely new.