In the service manual Yamaha specifies 14.0V at 5000 RPM as normal charging voltage. I get 13,99-14,0V at around 5000 RPM.

And regulated voltage is specified as 14,1-14,9V no-load. I guess Haynes specifications fooled me a bit, as I was expecting 14,1-14,9V on battery poles.

Guess its no point changing any regulator then. Would it be correct to assume that the bike acted weird due to a flat battery caused by drainage from connected accessories, and that it wouldn't charge due to being jump started from flat charge status?