well thats weird. The only thing pulling the clutch does is remove any drag on the engine. So it is more than likely the timing chain slap. The tensioners on these bikes are crap. They wear out all the time. The only way of knowing for sure would be to use a mechanics stethoscope on it or replace the tensioner and see if it goes away. The fact that it still runs nice and idles good means that your timing hasnt skipped yet but its only a matter of time at this point.
k..it seems like its a faster knock but it dosent seem to match the tapping sound from the top. and when i rev the motor the top tap stays but seems like bottom goes away..it dosent get loud and dosent seem to keep pace with the rpm's while reving. but the top sound does mtach the reving rpm's .could the top end sound cause the lower sound? the quad ben well taken care always had amsoil 20-50w oil, oil filter changed..but never had valves adjutsed ect.