MCT_MR2
What are the 3 letters for the plug going into the alternator?

Only reason i ask is some arent necessarily meant to have 12v on them.

yea true. most alternators i've worked with and wired up have battery volts on one pin in combo with charge wire to battery), 12 volt ignition on 2nd and the exciter (dash light) on the 3rd. 
 
hope you sort it out Eric. Possible to just run a aftermarket bosch universal alt?  wired up correctly with it's own circuit will do it's thing.