ex250, small engine noise

I have a 99 ex250 that i recently bought..It is a great running bike with only 4400 miles on it and it just started to make this small knocking sound only at low rpms-or just idling..its not a spark nock and i dont thinck its piston slap because it quits at higher rpm..I know my valves need adj..because of there small rattling they make....Im pretty sure ive narrowed it down two the bottom half of the motor.....It seams when it gets warmed up completley..the noise quits when i engage the clutch but as soon as i release it,it starts knocking again.....could this maybe be my clutch basket??? is this normal??
any suggestions would help thanks