I don't think it's the transmissions, neither is it the bellhousing or clutch, those are all proven parts. It's probably a combination of install error, or people simply not knowing what they're doing even with instructions on hand (some people still install these without aligning the bellhousing, a big NONO with these mdoern trannies, they have nowhere near the free play on the input shafts that for instance an old muncie has, they are much less tolerance to off axis positioning)
Then there's the issue that SolidLT1 brought up, and if his has it there must be others out there. The mismachined yoke will cause a vibration because the joint is not clamped down.
Then there's the obvious transmission & diff alignment. A lot of people don't do it with an inclinometer, do it by trial and error or not at all. Factor in the number of twisted frames and it's a recipe for problems.