http://www.wrrdualsport.com/tech-guide/air-intake <--- go here
Read through those instructions and see if you can figure out what you might have removed that you shouldn't have.
Or, reinstall everything you removed and see if the bike starts up again.
Without pictures of what you did it's hard to figure out what you might have done.
Can you take good detailed pictures of what you removed, and from where and then post them here?
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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