Timing gears/chain/tensioner is on the left, but I don't think I've ever heard of anyone having a problem?

Decompressor pin loose or broken? - Known issue, but not that common.

Alternator? - Unlikely.

Starter motor gears and sprag clutch?

Gearbox???

Can you describe the noise? Knocking, tapping, rattling, squealing... Might help narrow things down a bit.

Use a length of hose as a listening device to locate the exact position of the noise.

It's also worth noting that the upper of the two bolts the hold the exhaust heat shield on is too long on early bikes and taps against the exhaust pipe at certain engine speeds.

http://www.xt660.com/showthread.php?t=18033

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