+1 on checking the connections. Intermittent issues point towards a dodgy connection. Then do the direct wiring from the R/R to the battery and direct earth to the battery with heavier gauge wires. You'll get much better charging and battery performance.

Is you bike EFI? If it is then your battery might be hovering around 80% charged. The computer on an EFI bike won't let the bike start if the battery charge falls under 11.6 volts.

Cheers, Richard
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09 America, Staintune Pipes, K&N, Breathe, Hagon Nitros, AI & O2 removed, tune 20184 (modified), MTX-L a/f gauge