If you run it up on stands you "might" be able to see something but it could be misleading because with the tires unloaded, they can create vibration that normally isn't there.
Lets think about this methodically; you know you have a vibration, it has to be coming from some place. The challenge obviously is trying to find it, you know its there but it is being illusive. The vibration is coming from something rotating (obviously); start at the most likely and then go down the line. Any drive line vibration causes me to look at the U joints automatically as a starting point, then wheels/tires, then axles. Since the wheel/tire combo is unchanged, you can probably discount them.
Here's a question, are you sure you have the right U joints; seems pretty intuitive but thought Id ask. How about a bad pinion bearing?