If I were keeping stock exhaust, I would NOT remove or disconnect EXUP.
The EXUP does not rob performance, and some say it helps with low range.
That's just me though.
You can do flapper mod.
Gearing change would be something you could do, although that messes up your speedo without also buying a speedo correction device.
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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