All Gpx 2fiddies and even the KLE500/GPZ500/ER5 motors share a similiar knocking noise. It's a concern till you line up next to 20 others and hear the same noise!
You mention yours dissapears when the clutch is pulled in. This could be a little Clutch basket knock. It happens commonly also. They are a pretty good engine and providing the cam chain is not rattly, and you change the oil regularly they will go almost forever. Watch cam chains, I have seen a couple eat there way out of the engine cases!!!!
It's not funny, but hard not to laugh when a rider comes in and says there is oil leaking from the front of my motor!!! London to a brick it's cam chains hanging in the breeze!
FWIW, I sold a GPX250 with 88,000klms (one owner with a full workshop history by Kawasaki) to a guy who did another 80,000 klms on it before it needed any rejuvination internally. It went throu a few cam chains in that time, but bugger all else!
"I hate to advocate drugs, alcohol, violence or insanity to anyone, but they've always worked for me" Hunter S. Thompson.
There are really only two questions in life. 1.Which way do i go? 2.What is the lap record?