I've got 3 different methods for stopping my XR650R engine, dependant on whether I need to check the oil level or not:
1) Kill the engine as soon as I stop
2) Stop, let engine idle for 30s, kill then check oil level
3) Pull clutch in 200m before a gas stop to let engine idle for 30s, roll to a stop then kill engine, check oil
If the engine is not allowed to idle for 30s before checking the oil then you will likely get a false low oil level and overfill, which will result in an over oiled air filter causing rich running & possible overheating and possibly causing the counter shaft oil seal to blow.
The cooling system is *not* effective unless the XR650R is in motion, so it will get hotter, eventually overheat and boil out it's coolant if left to tick over on the side stand (about 15 mins in England in winter!). The boiled over coolant will be captured by the header bottle and sucked back in as it cools - an invention of the Light Car Patrols and Bagnoll/Bader in the Libyan desert)
The cooling system is effective on the move - so long as the XR650R is not a restricted model (North American bikes are restricted ex-dealer) and the jetting is right. De-restriction is relatively cheap and simple (loads of info is available at http://autos.groups.yahoo.com/group/XR650R
).European and Aus XR650Rs are generally unrestricted although some North American bikes are sold new in Europe and Aus bikes are restricted ex-factory. If you have a 40mm tail pipe tip then it's not restricted.
The pre '03 XR650Rs had a couple of easily improved weak spots; upgraded parts are available - the clutch bushing is prone to seizure & the counter-shaft seal (behind the front sprocket) will easily blow out and dump the oil if the engine breather gets pinched (& possibly by overfilled oil). However IMO both these points are related to abuse, I have not pre-emptively fixed mine, but you may feel differently.
[This message has been edited by Ian Bradshaw (edited 24 August 2003).]