How do you fix this?

Must be a B or E trans then, as the shifter is mounted out at the end of the tail shaft.
I suspect the vibration is due to the alignment of the yoke to the drive shaft. The trans needs to go up just a bit to give a nice straight shot from trans to driveshaft.

The car runs quite well and shifts great. If I could figure out how to raise the trans a bit, and sure things up, I think it would do the trick.