OK, here we go
"The stock XR650R was first delivered in model year 2000. The stock bike had several significant problem areas, all of which have had solutions discovered by the riding public. Below are the known problems and their recommended solutions.
1. BOILOVER - the stock bike intake and exhaust are highly restricted and the carburetor is jetted very lean to meet emissions laws. This combination causes the bike to run hot. The bike is also delivered with a radiator cap with pressure relief set at 1.1 bar which provides minimal margin for boilover. The solution is to "uncork" intake and exhaust, rejet the carb accordingly (see getting it to run right for specifics), and install a 1.6 or 1.8 bar radiator cap.
2. CRANKCASE BREATHER - the breather hose is routed from the engine to the airbox between the gas tank and the frame with very little space margin. Should the line become pinched, the typical result is a blown sprocket shaft seal and oil all over the place. The solution is to make sure the breather line does not get pinched, by either rerouting or applying silicon lube to the line in the problem areas.
3. CLUTCH BUSHING - due to lack of lubricating holes, the stock bushing can become seized to the clutch shaft, resulting in the bike being stuck in gear. The solution is to replace the stock bushing with Honda part 22116-MBN-671. When running the stock bushing, minimize the time the clutch lever is pulled in when stopped etc.
4. CRACKED FRAME - this problem does not appear to be widespread, but has been reported.
5. FOOTPEG BOLTS - the bolts attaching the right footpeg can bend and ultimately break off. Periodically check and replace as required.
6. YOSHIMURA EXHAUST - the yoshi exhaust comes with mounting points same as stock. Do not use the one near the right footpeg or the pipe will crack. This happened to me so I cut the weldment off the pipe and made a sleeve patch with stainless steel 0.030 sheet stock. Pipe has been fine ever since.
7. IGNITION LEAD - the high voltage lead going from the coil to the plug runs close to the frame and can arc to ground. Fix is to apply extra wrap around the lead, like electrical tape.
8. MACHINING CHIPS - reported by several users, aluminum chips from a milling operation found on screen in down tube. I personally have also found chips, and lots of them, stuck in the oil passage feeding the cam. These are definitely leftover chips from manufacture, and not from any sort of failure.
9. AUTO DECOMPRESSOR - lifts right exhaust valve off seat improperly causing buildup of carbon on valve seating face. Deposit is so hard valve must be reground to remove. My solution was to remove the mechanism and install a sleeve. Others have removed the mechanism and welded the oil holes closed. "
