Are the mounts for the Mercedes engine or some other mount adapted to your needs?

Vibration can come and go depending on RPM ( like an out of balance tire that is smooth at some speeds. ) without being able to see / feel / hear the motor I can't say if the flywheel is the problem or not.

What year / model Jeep ?

Have you ever run a 4 or 5 cylinder diesel before? Diesels with few cylinders tend to vibrate alot.

If the idle is set too low vibration will be worse, perhaps yours is just running too slow.