Differences Between Years
The Honda XR650R was produced for seven years. There are virtually no mechanical differences between these years of production. The only significant mechanical change during that time was:
In late 2001 the clutch bushing was updated with venting holes and a thin galley way to improve oil flow and prevent binding and sticking, particular when the bike has been left sitting. This is a very minor change and is a very simple and cheap fix if you happen to have one of the early models.
The original bushing part number was #22116-MBN-670
The replacement bushing is part number #22116-MBN-671
If this part hasn’t been replaced on your bike it is a good idea to do it before it fails. Failure of the bushing under stressful conditions can damage both the clutch basket and the shaft, so better safe than sorry.
The only other changes to the bike over those years were to aesthetics. The seat cover and tank graphics changed a couple times during production of the bike, but of course that has no effect on performance.