What are your pinion angles?
If you don't know....then its probably the problem
My old bagged minitruck used to love to rumble at various heights, because raising and lowering the truck changed the pinion angle.
When you do a swap, depending on the engine and tranny xmember position, and length of the DS, you can end up with a WAY different pinion angle than what you started with. This will wear out ujoints, and in a high hp application can be a huge annoyance.
Does the 2 piece shaft use a carrier bearing?