I wouldn't describe the noise of worn Ujoints as "chatter". More of a clunk, and you get it when loading or unloading the driveshaft. In my (limited) experience clutch chatter comes from a tired clutch. You fixed that. A rough flywheel. Did your shop machine it? Was it grooved?
Other things that could give the symptoms might be motor mounts, transmission mount, oil on the flywheel, or some non-specific alignment problem caused when the PO tried to get cut in half by a semi. Stiffness could be a pilot bearing, throwout bearing or linkage. Some of this stuff should have been inspected by the shop who did the work. If the flywheel is grooved, but not too badly, it is likely that it will wear in eventually, but it isn't really right. Bet someone else knows more than I do, though.