Another thought. With an engine swap, the centerline of the crankshaft and the centerline of the pinion need to be parallel, both vertically (which you have experimented with by changing pinion angle) and laterally. They do not have to be perfectly in line with each other, just parallel. Some early big block cars had the front of the motor shifted to the right (passenger side) to give more clearance for the exhaust/steering on the left -- making the crank centerline non-parallel laterally with the pinion. I have seen driveshafts for those cars with the u-joint yokes factory-welded slightly out of phase (10-15 degress, as I recall) to minimize vibration -- definitely a crutch. You have probably already checked, but I would make sure things are parallel in both planes. Good luck.
Pappy
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