Top picture almost looks like the EXUP servo connector. But, you'd be getting an error code if it was just stuck under seat like that. I have no idea what that could go to. Do you have stock exhaust? I'd guess not since it looks like the usual flapper crap is all gone.
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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