So the full exhaust system was on the bike and it was running fine with no CEL for some period of time before the Yosh doo-dad was installed?
If that's the case I'd guess it's not the EXUP servo motor error light.
I have to wonder if there's a vacuum hose not connected properly somewhere.
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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