Need Help! - still trying to solve noise/vibration issue
 

The car is a 2001 A4 Quattro, 1.8T, 5spd. It's got about 56k miles on it. About a month ago I started noticing a loud clunking/vibrating sound in the front end whenever I was at a dead stop and would start to slowly let up on the clutch. Mechanic diagnosed a bad throw-out bearing. During clutch replacement they determined the transmission's input shaft was damaged - so, I ended up getting new clutch and a used tranmission put in.

I got the car back, and it seemed better for a while. Then the sound came back, but a it's bit different now. Plus, now I can feel feel a constant vibration - in the stick and the pedals - it's especially noticable when I'm taking off. I can also hear and feel the sound now at all speeds, though engine noise drowns it out a bit at highway speeds. Before the original problems with the clutch, the car was always really quiet. Two other mechanics have looked at it (including the dealer) and no one seemed to know - or agree - if it was anything to worry about or look into further. So now, I'm just frustrated. Something's not right.

I'm sure it's not a wheel bearing, I've had those go before. There isn't anything noticably vibrating under the car. I had the engine and tranny mounts checked and tightened, and they seem to be fine. My only thought now is maybe CV joint? I know they start making a clicking sound when the go bad and while it's not exactly what I'm hearing, I still wonder if I should have it checked out. It doesn't make a distinct clicking sounds when I'm turning though. Drive shaft maybe? Any thoughts/help would be much appreciated.

-TS