It had this exact same problem a few weeks ago, then quit with a new battery and starter, then started up again...
Very odd.
In that case, it doesn't sound like water in the gas.
Maybe some sort of electrical fault - something shorting against the tank? When working on the bike and the tank off, the wiring got moved enough it took a while to vibrate back into position?
I think you're going to have to take a close look at everything - poke around and play detective. Sounds more like an intermittent problem at this time, and intermittent electrical faults are THE worst!