vibration after 3.23 to 3.91 swap

Remove the driveshaft and place a straight edge near the pinion yoke. Rotate the pinion and see if it spins true. I've seen the forward threads on the pinion bent from people beating them with a hammer. You should have to lightly tap the 1350 into the yoke, if it slides in to easily something is wrong. Just because your driveshaft is new doesn't mean it's straight so check it out. Also check the u joint phasing.