This machine is definatley not charging!!!! You lose the spark if the voltage drops. When the engine is under load the spark will fail completely.

Check that everything is plugged in properly at the alternator side, also the regulator plugs. It could be that the regulator is buggered!

There are a lot of plugs and wires coming from the clutch LEVER side casing where the front sprocket is, just follow them up into the bike and make sure that all is well.

I dont know of any methods to test the regulator (also known as rectifier) apart from what you have already done with the voltage checks, but chances are this is where your problem lies. Im sure someone here has a spare one you could try on the bike for a bit.
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NSR250R MC21 (NEARLY SOLD!!)
VFR400R NC30 (SOLD)
Santa, please bring me a NSR500 and a SP-2 next year. Pleeeeease....