Strange C4 body vibration

About a month ago my 1999 C-4 bottomed out as I drove 5 mph through a chuck hole in rain drenched parking lot. I'm not sure it wasn't there before, but after the incident I began noticing a strange vibration through the clutch pedal whenever I would shift through the gears, particularly at the moment the clutch pedal is first depressed and when it meets the floor board. I also noticed (again, this might have been present beforehand, but at this point I was looking for any related problem) a subtle body vibration at 2,600-2,800 RPM, in third or fourth gear. It seems correlated to RPM, not speed, and I can't seem to feel it in first, second, fifth or sixth gears. The service manager at the Porsche dealer says all C-4's have a clutch pedal vibration to some degree. I've gone to a private Porsche mechanic, who checked the motor mounts (OK) and dual mass fly wheel (OK). Next he plans to check whether the underneath cover is vibrating. He calls it a body hum, almost as if engine vibration is transferring to the body, which is probably why he thought motor mounts at first. He's not sure the clutch pedal vibration and body vibration are linked. He doesn't think the bottoming out incident is the cause of the vibration. At this point, he can only think of one other thing to check -- shifter linkage. Even he admits the vibration may be unfixable, perhaps a symptom of C-4 ownership. Any ideas? This car is so remarkably smooth otherwise, I'm annoyed by the vibration. Incidentally, I put new Michelin Pilots on a month ago -- I went one size wider to 18/30/285 in the back -- and the ride quality is terrific.