Not to hijack but I'm having a similar issue. Picked up this bike the other day and the wiring is shot.
I've got 6 wires running out the side.
1 & 2) These two black and red wires look like they were cut so I've attached them together.
3) Green - assumed negative/ground
4) Solid red - assumed positive
5 & 6) Solid red with fused - looks attached with fuse on purpose.
I'v referenced the shop manual and as best I can tell I should run red (#4) and green (#3) straight to the battery?
Is this correct? Am I missing anything?