What numbers are you running on your programmer?
Quick answer - an FmF programmer can ONLY add fuel. It can't take it away.
I do find it hard to believe you're too lean rich if you've removed airbox door and replaced the stock exhaust with something less restrictive.
Really need to know what numbers your programmer is running.
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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