hi axt, have you checked your valve timing?. the pivot on the tensioner guide broke on mine and it may just explain the noise and lack of power. mine was out a tooth,
as i ride like an 'ould woman' i did not notice the power loss. checkout http://www.xt660.com/showthread.php?t=17351

I will pull out gearbox,but i have no time right now,you know job,wife,kids.....:009:

hi, the parts i was suggesting are veiwable from the generator side

Before stripping anything I would be diagnosing in what area the noise is coming from.

Known faults relating to noises in the 660 motor that I know of there might be others but these are the ones I have documented over the past 5 years. They failed for various reasons some were by abuse from not servicing.

1/ Lose tappets, many
2/ Main bearing failure, X2
3/ Big end failure, X1
4/ Cam chain guide plate broken, X1
5/ Decompression pin broken, X1
6/ Gearbox output shaft broken X2
7/ 3/4th gears broken, X2
8/ Worn piston & bore X2
9/ Clutch nut lose, X1
10/ Primary gear nut lose, X1
11/ Bent inlet valves, cotter broken, X1

I�m highlighting this thread since I have a rattling sound on my bike. It has ran 35000 K since march 2011 and I�ve done all service required on the bike and this sound appeared 3 weeks ago, I haven�t driven it since.