I have no AIS, no airbox door, an FmF Q4 pipe (but it does have the spark arrester in still), flapper mod, and stock Yamaha air filter.
I've never had a stalling issue.
My idle is never rough.
Could it be an idle speed adjustment you need?
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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