I would guess at the bushes being worn in the engine torque arm. It's on the left side of the engine and mounted on the left end of the swingarm pivot.
If you look just behind the front sprocket you'll see the little arm.
Matt from Tyga wrote of the same symptoms you are experiencing. He ended up stripping and rebuilding the gearbox, only to find it was the torque arm.
It's there to stop the engine twisting as it's rubber mounted.
Only problem I can see to you fixing it is, I think it's now unavailable new.
I'm going to look into getting mine rebushed when it's necessary.

I think the rubbers on the clutch that you are talking about go on the inner friction plate to act as little dampers. They are little oblong shaped things.