Not aware of any changes between 2008 and 2013 to any parts of the bikes.
Other than colors of plastics, all parts should be interchangeable.
There are a few differences between the X and the R on things like the wheels and front brakes.
There are frame color differences between the X and R.
Maybe that's what the part number difference reflects?
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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