ok i have 62K miles on my 98Z28 M6 w/stock clutch and lately ive noticed a knocking sound coming from under the car....you can feel it in the shifter as well) at first i thought the bottom end of the motor was knocking but know now its the tranny!!! the shifter does chatter when letting the clutch out in 1st gear(flywheel needs turning most likely) but other than that it shifts fine (a little noisy going into the gears) *when the clutch is depressed, the knock goes away mostly, but when the clutch is let out, the knock is pretty bad...any suggestions???
the only thing aftermarket on the driveline is the Pro 5.0 shifter

 

So when the clutch is engaged, you are hearing the sound? Only at idle, or all the time? It could be that the clutch is slightly warped, or it could be your pilot bushing. I'm not sure what it sounds like when a pilot bushing/bearing goes south, but hopefully someone will chime in. You could have gotten some oil on your disc and warped it. Also, it could have been burnt by slipping. Does it ever slip? Have you badly slipped the clutch racing or anything (like off the line)

 

the tranny makes this knocking sound most* of the time when clutch is in neutral and sitting still.....it sometimes even does the knocking when clutch is pressed in too....any suggestions appreciated....Jeremy