It'd be nice to know how many miles are on the car, as that can be indicative of a part's normal lifespan. Then again, driving style by various owners can be a huge variable. Did you get maintenance records?

Is it a single clunk? Or a series of clunks?

Pretty hard, in some cases impossible, to check a U-joint with the driveshaft bolted up. They can be tight, binding.. etc. If that's what it is, it will get worse in very, very short order. When it's ready to completely fail, you can see it and/or feel it when bolted up, but waiting can be a fine way to ruin the yokes on the driveshaft itself.

My first guess is rear-most U-joint. Second guess is the carrier bearing and/or bushing.

I've never heard of the rubber donut shrinking, but what you describe does not sound right.
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-Matt I ♥ my ♂