nocking up me frame

Hi all you apers out there, just a quick line to ask some advise about a mysterious clunking noise and feel whilst on me bike.Im sure its not bearings cos it stops when you pull the clutch lever in,and is worse when its cold it also disappears above 3k rpm.IM running a rp58 chip it was already init when i bought it,have tryed changing it back to standard but no difference in the noise.A kind chap told me some information from this web site over the phone but i have forgotten most of what he said .Can you explain again paul or can anyone else help.