I had most of the connections labled when I pulled the harness, but a couple of them have lost their lables. This wire comes off of the rear of the harness, and has the end pictured. Any tips as to where this shoule be connected to?

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I would bet that it connects to a PO created ground. That is definitely a non-factory wire. Try running the engine without it connected? Maybe is unnecessary.

BTW: I like your signature . . . Zen and the Art of Motorcycle Maintenance is a great book. I is kinda weird though, I got it from my girlfriend's dad for some reason

Find the other end using a meter or continuity light. Then find that pin connection on the wiring diagram for your year. That will tell you where the loose end is supposed to go.

The diagrams are in the Haynes manual or on the Pellican Board.