Same thing happened to me. I ran the fuel tank very low. The problem with mine was, the fuel filter. You see, the bike will suck up the gas, and it has to go through the fuel filter. If it's not a clean filter, then you won't get enough gas flowing through and it will seem to die on you. And sometimes it does... Then when you start it up again, it'll fly until fuel gets backed up because it can't get through the filter.
Change the filter. It should be located where you fill up the tank. You can get a filter at the auto store for a couple bucks. Let me know if that's what it was! I'm almost positive it is the filter because what's happening with your bike sounds just like what happened with mine!