Don't worry about the harness from the stator at this point. My guess is that you have two harnesses coming from the stator, and the other one connects to the CDI, etc. The harness that changes to one wire is likely to be a shift indicator, which is not stock equipment on many bikes, and it's just fluff.
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Weldangrind
"I figure I'm well-prepared for coping with a bike that comes from the factory with unresolved issues and that rewards the self-reliant owner." - Buccaneer
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