Check the wiring out of the regulator. The black/red wire may be wearing through the insulation against the frame, sometimes shorting and sometimes not. A series of short circuits will drain a battery. Also check the voltage at the battery. At 5000rpm, you want to see between 13.5 and 14.8VDC. You could have run through 2 stages of a failing diode too. The first stage lets current run in both directions instead of just one and causes a short circuit, blowing the main fuse. The second stage completely burns out the diode so current runs in neither direction, creating an open circuit. That will eliminate 1/3 of the charging power.