From what you describe, it sounds like something is vibrating at the fundamental frequency of the body shell. That will make it hard to locate, because the vibration source can be small, and need not be in contact with the shell.

One thing to check is driveline alignment. Mercedes shafts will only work without vibration if the transmission output and the diff are exactly in line. It's not sufficient for the crank flange to be in the same plane as the diff flange, it has to be directly opposed. Otherwise, the u-joint creates a wobble which can be felt as a vibration. Unlike a two u-joint system, you can't depend on the driveshaft to absorb any misalignment.

My other thought is that this is related to the turbo or exhaust. You might try blocking the wastegate open as a test, and see if that makes a difference.