Strange Clutch noise on 03 GT

I purchased an '03 GT a month ago with 18k on the odo. In the past week or two, I have noticed a ticking noise (not as quiet as injector noise) coming from the area ot the bellhousing/tranny. The clutch engages pretty close to the floor, does not seem to slip under heavy acceleration. The noise comes on only after warming up a bit.. only when clutch is engaged. I feel a little vibration in the shifter (Tri-Ax). I know the short shifter is not vibration-isolated, but this seems odd. Does this sound like a clutch diaphram issue?
 
I've got a racket in my 02 GT but I'm not sure it's the same thing you hear. In my car, it's most noticable cold. With the clutch pedal down and the trans in gear I get this "cylical rattling" noise that I can "feel" in the shifter. If I put the trans in neutral and release the clutch, the noise goes away. When the clutch is depressed again, the noise will return, quicker if the trans is slipped into gear.

At first I thought it might have been a crank thrust bearing (loading it with the clutch trying to push the crank out the front of the engine) but I'm increasingly thinking it's the clutch disc "battering' around between the flywheel and pressure plate and the gears in the transmission knocking against one another as a result. When I kneel down beside the car the noise definitely seems to come from the trans/bellhousing area.

I recently had the TR-3650 TSB work done and they (Ford dealer) assured me the release bearing was fine so I don't think it's that.

When you say the noise is there "only when clutch is engaged", you mean the pedal is completely released, right? If so, it's probably nothing to worry about. Might just be the release bearing and release arm "chirping" a bit as a result of some runout in the pressure plate diaphram. If you touch the clutch pedal (press it down, say, 1/2-inch or so) does the noise change or go away? If so, it's probably nothing to worry about. If the noise was a squeal or rumble with the pedal on the floor I'd suggest the release bearing was smoked.
 
Trinity-GT.. thanks for your reply. The noise is more prominent when the clutch pedal is out. As with your noise, I can feel the vibration in the shifter as well. The performance of the car overall has not really been affected by this vibration-noise.. was hoping it was not a broken finger of the clutch diaphram or trashed throw out bearing. Thanks again for your input!