When you say "ran her dry" do you literally mean you road the bike until it completely ran out of gas?
If so, I'd imagine it's possible you got air into the fuel line and that might possibly be an issue until it's completely purged.
How far, or how long did you run the bike with the "cutting out" conditions?
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2008 WR250X
Gearing: 13t - 48t
Power Commander 5 / PC-V
Airbox Door Removed - Flapper glued - AIS removed
FmF Q4
Bridgestone Battlax BT-003rs