A clunk when going to drive certainly could be the differential, but the U-joint is the most common cause there.......I wonder if they replaced that too?
Turbo GS300 brought up a very good point, and you will find a BUNCH of different threads on this board about this same "GS400 vibration" problem. It really is common.
By the way, mine does it too and if you are on a flat road, and it's quiet, you can barely feel it at even 40mph. (and 50, 55, etc) up to around 80mph where it clears out a bit.