Can you describe the "clucking" a little better?
I have an 03 200 with makes what I would describe as a light knocking noise at idle and low revs, but seems to disappear under acceleration. I had read that this appears to be normal and even heard another KDX on youtube that made the exact same sound.
Then my brother bought an 05 220r and it is silent! My bike runs perfect, so I am not worried about it so much ... but it would be nice to have her quiet if I knew exactly what the culprit was.
KIPS seems to be the answer so far, but the sound seems to be coming from a little lower in the motor.