Scotty
I think you have hit the nail on the head it is the 2 non-red-or-yellow wires which are the problem.
The original Reg Rec uses the frame as earth the othter wires are
1) a feed from the battery to give charge control
2) the feed from the voltage regulator light -
so they can't be wired to earth - that would be a radical change for a replacement part.
The risk of total burn out of battery ,loom & reg rec seem very high here.
,.
was yours a 2 wire alternator pre 98 monnie?
Jon