Well, I unplugged the wire for the parking brake and it has seemed to fix my issue. Quad starts up with out the clutch, and doesn't break up when I hit the throttle. Neutral light still doesn't work though. I won't be able to ride it until next weekend, instead I'll be racing the 69 Camaro this weekend at the track. Thank you so much for your help.
Just to recap my issues and the fixes.....
Carb needed to be upped a size on the main jet, and air fuel screw adjusted.
Wiring harness was replaced, as well as neutral switch, stator, and starter clutch.
Bypassed the clutch switch by plugging the wire harness side into its self, and parking brake set up removed.