I just went through this with my truck. I had done a transmission swap, followed by an engine swap, followed by a rear axle swap, and always had a persistent vibration. Turns out the pinion was at 2 degrees up compared to the transmission. A cheap set of 2 degree wedges has nearly eliminated the vibration. If the angle is off, it is better to be off in the downward direction. As torque is applied, the pinion will rotate upward.