Ok well I swapped the harness, and most of all the problems went away.
The only thing left is for some reason the ABS+TCS lights are on, but I think it might be the connections at the wheel, didn't check over there really good before putting the wheels back on, this is last on the list atm.
Other thing that's still wrong is the Alternator is still not charging, no light though. I cheaked over the fuses and there fine, have been doing a few others to see if its a wiring issue before I pull it and do see if its bad. If it is bad, is there a chance that I can split the case haves and swap with the alternator internals out of my 2000 GT?
Last problem as of right now is a coolant leak, internal one at that. Its either the Supercharger gasket or LIM both I replaced and I'm thinking one or both didn't seal. Don't know what I can do to check on either or what to do to try and make them seal. And no the Supercharger gasket is not the Gearlock stuff, I did buy one of those but it didn't have the O-rings so I got another set from Advanced.
Thanks for any help
