The Honda XR650R Thermostat is known to fail regularly. This isn’t a drastic issue, but will cause your engine to run under non optimum temperature conditions if not treated. It’s a good idea to check your thermostat from time to time and if it looks something like the photo below then it is time to be replaced.
From time to time it’s a good idea to inspect your clutch bushing for wear. Wear can create slop in the clutch and over time significant damage to the basket. These parts aren’t known to wear at any accelerated rate, but next time you replace your clutch plates make a point to pull off the basket and have a look. This is what you’ll see when you remove the XR650R clutch basket.
Follow the directions in the service manual available on this site.