I'm pretty clueless about the deep inner workings of the KDX clutch (though I am learning slowly), but one area I think you should look into are the mechanicals and bearings associated with the kick starter mechanism...
I have a 2004 KDX-220, and the bike rattles and clicks and taps up a storm right after I start it (while the kickstarter is still out and presumably "slightly" engaged) But as soon as I flip it into its stowed position, the idle is chatter and rattle free!
Not certain if just having the kickstarter folded out somehow sets up some kind of vibration harmonic that makes an internal vibration worse, or if the fact that when the starter arm is out it causes the kickstart shaft to drop a bit and engage ever so slightly.
When it gets time to service my clutch, its a sure bet that I will be looking at this area very carfeully to see if i can identify whats going on, but for now, all I know is that while the bike is running, flipping out the kickstarter causesall kinds of rattling, and flipping it back in kills the sound...
Good Luck!
-Feanor