"This thumping noise started during winter shortly after I had my flex discs and support bearing replaced."

The fact that the thumping seems to be dissipating as the weather gets warmer suggests that it is being transmitted through a rubber mount of some type. The cooler the rubber, the stiffer it is, the less it absorbs.

Seeing how it started in the winter and after your support bearing and flex disc replacement, I wonder if whoever did the job, lined up the drive shaft halfs correctly. there should be a double notch on one side and a single on the other. Put the single between the double for correct alignment.

Also, if the diff was replaced or removed, were all the shims reinstalled for the front mount? what about the rear diff to subframe mounts? are they sagging or cracked. (they are rubber as well)

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Scott