OK, last update (I hope).
After battery and stator tested OK, the damn rectifier/regulator would seem like the only possibility, but my tests were inconclusive. Hey, what can I say...electricity isn't my thing. So I took it in to a professional who went through his own check list to come up with a bad regulator/rectifier.
Total damage:
R/R = $166
Labor (not including mine) = 2 hours at $110/hour
Overnighting a part from Yamaha = $50-80????
Still being able to fish the coming weekend = priceless!
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Oh, and I have no idea of the gender or age of the mouse. That seems to be taking my rodent adventures just a step farther than I care to go.