Put a good voltmeter on the battery to double check your readings. Check your battery connections, make sure they are clean. Load test and do a voltage drop test on your battery to make sure its OK. Check your battery cables, if you have a load tester, this is easy to do, if not, feel the battery cables from one end to the other, pay attention to where it goes thru the cowl. make sure you don't have any hard spots. Japanese electrical use very fine strand wire, it works great till it gets overloaded, corroded, or old. I replace Yamaha battery cables on a regular basis. Try using a set of battery jumper cables to add current carrying capability from eth engine to the battery and see if it makes a difference. Keep in mind, the regulators are fairly crude, they generally operate in an on and off mode, where as if it needs charging, it turns the charging coils on and it goes full voltage, if it doesn't need charging, it goes off, so its common to see big swings in voltage rather than variable output like an alternator would show.
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