My 1999 C5 coupe developed a rattle noise from the front of the engine. I took it to Mr. Goodwrench where I purchased it new and had the car serviced. I was told the a/c belt tensioner was bad - I authorized repairs. Then, the dealership called and said the noise was a bad power steering pump. I authorized repairs.
When I picked up and paid for the repairs, the same noise was present. I left the car for more diagnosis (technicians - not mechanics, don't forget it!). The noise was caused by a defective decoupler pulley on the alternator. The alternator was replaced (for very little cost since I screamed loudly regarding the two previous items that were replaced and were not defective). Noise gone.
My point in this long story - noise can fool almost anyone. The decoupler pulley noise sounded to me like a defective water pump bearing. Does your car have the revised alternator with decoupler pulley (which eliminates the A4 shift rumble)?