I'm worried about the "runs rough at times" more than the vibration.
It may still be the nikasil engine ... look into that; check the casting numbers on the block. You do not want a rough running v8 ... that can only mean trouble. Read this and look or have a mechanic check the numbers BMW M60 - Wikipedia, the free encyclopedia
edit: If it is a newer, Alusil block, have a leakdown and compression test performed ... something doesn't add up here: '94 530 for 2000. I paid more for a '90 535.
As for the vibration: if the clutch is already hooked up, it's more than likely something to do with the driveshaft. Possibly:
- Guibo/flex disk gone or installed backwards/out of alignment.
- Worn carrier bearing
- Incorrectly adjusted preload on the carrier bearing.
Hope that helps.