Yoke phasing

Have you measured the angle between the pinion axis and ground and the transmission axis and ground? They need to be about the same angle (reversed) or the pinion can be up to a max of 4 degrees closer to the ground so that under full load, it rotates up to the same inverse angle as the transmission.

If you've done this measurement and they're good, then start worrying about syncing the universals, but yes they should be identical.