Do I understand correctly? Did this start when the driveshaft work was done? If so I expect that the drive shaft was not matched up with the spline correctly losing its balance. This is showing up in the transmission.

BTW. These transmissions do not use differential gearlube. They use engine oil or ATF. My 240D still has the original manual transmission after 533000 miles. Several hundred thousand miles ago I put 10W30 Mobil One in and have used nothing else since. The gear oil will make it difficult to shift in the winter and cause it to get very hot in the summer. I highly recommend changing it.

It would be worth a try to pull down the driveshaft, mark the two sections at the spline joint in the front shaft, disconnect the spline, turn it 180 degrees and put it back together. If it is that bad out of balance it is probably a full 180 degrees off.

Any time the driveshaft is removed, it should be marked at both flex disks and the spline joint and put back together in its original orientation.

I can't imagine what could be causing this that's inside the transmission.

Best of luck,