Anyone ever figure this out???

 

Still trying to figure this out has the problem been resolved?

 

After reading the whole post, it read almost exactly like my car. 1996 A4 B5 1.8t Quattro will a 5 speed manual gearbox.
Thunk when changing gears, decellerateing or lifting off or using the accelerator.
I went to three specialists, who put it up on their hoist, checked every element of the drive-line, engine mounts, gearbox mounts, diff mounts an conducted a road test.
None diagnosed the issue precisely, as they all said there was a bit of play in most components, given the age of the vehicle.
Rather than replace all of the old components, I decided to wait, while driving as smoothly as I possible could.
Front Drive Shafts eventually began to click when turning the steering wheel lock to lock.
After the Front Driveshafts outer CVs were replaced, thunk when changing gears disappeared entirely.The CV outer ring had worn and elongated ball receivers. The clunk was caused by backlash within the joint, which was quite difficult for the three specialists to diagnose accurately.
A pity that I didn't take any photographs of the worn parts.