The noise that goes away when the clutch is disengaged is the clutch, the transmission gear lash, and probably the primary chain slap. The latter is not disengaged but inertial loads have changed.
Next would be to isolate the location of the noise that remains. If you take a long screwdriver and hold the handle in your ear socket, you can probe with the tip of the driver and find where the noise is the loudest. Is it from the bottom of the engine or nearer to the valve cover?
Have you adjusted the cam chain tension properly? Is the lock down bolt tight? Does the jam nut turn free of the adjuster stud during adjustment.
Carb sync, as well as general engine tune, effects the intensity of each cylinder's power stroke. If not even, the crankshaft rotational velocity changes within the firing order cycle. Any chain attached to the crank then alternates which side is slack. There are two; the cam and primary.
These bikes need a complete tuneup every 3000 miles. Have you adhered to the maintenence schedule? When was the last tune up?
