When I took the old ones out they were not in the differential case at the same position.  Actually they were darn near exact opposits -- so if one flange was up and down the other was side to side. My car did not have a vibration - I can't imagine that the yokes would need to be in the identicle position or exact opposits....I don't think that's your vibration.  Maybe an out of balance drive shaft?  or your bearings?

The side yokes do not need to be clocked, or in the same position. They will rotate at different speeds in turns, so they will naturally be in different positions all the time.
Rarely will a halfshaft create a vibration, unless it is bent, or the u-joint is damaged/worn out.
The most likely cause of driveline vibrations is the trans mount, or the front diff mount/cushion, assuming that all of the u-joints are in good condition. With the diff and trans mounted firmly, anything that causes the driveshaft to be out of position to the side, or up/down, in relation to the yoke on the diff will cause a vibration. If the trans mount is soft/broken, it will allow the driveshaft to run off to the side, and the same with the diff mount/cushion if it is broken/worn. 

I didn't think of the trans mount! I will check that next time I get it up in the air again. If it is like the rest of the rubber suspension on the car I am sure its bad.
Thanks dude!
Rich