I think you'll have to remove the u-joint cover and inspect that. If the shop didn't refill the u-joint bell it may have already worn out. It's a bushing type u-joint (no needle bearings like modern u-joints) and relies on the transmission lubricant in the rear half of the transmission for lubrication. It's also possible that the shop didn't get a seal behind the new torque tube/shaft bushing installed correctly and the lubricant has drained out into the rear axle. You could pull the rear differential fill plug to see if it's overfilled.
My money is on the u-joint being the problem.
I'm also suspecting that the "self clearing" comment by the shops was just a way to blow you off.
Most noise issues don't fix themselves, especially ratcheting type noises. They usually get worse like yours has.
