Before you go out and get a replacement engine, it is worth checking the crankshaft nut behind the clutch side engine cover. The nut can work itself loose and make all sorts of horrible noises. It is a known issue.

If you get to it early enough and re-torque correctly there is unlikely to be any damage caused and everything will return to normal.

Have a look at these two threads:

http://www.xt660.com/showthread.php?t=20263

http://www.xt660.com/showthread.php?t=20512

Could well be this nut, in which case, an hour in the workshop could save you a fortune and get your bike back on the road quickly.

__________________