Take a close look at your transmission cross-member mount and motor mounts, anything with a rubber/poly bushing, along with all related bolts/nuts. Actually stick a big ass pry bar somewhere in there and move the entire drivetrain around while you look at it. A rubber/poly mount, even new ones, can be totally blown out, but almost invisible to the naked eye when the truck is static. A bit of torque is all it takes to expose those. Or, have someone in the seat, cycling through the gears while you watch the mounts.
Tighten all (at least put a wrench on them) crossmember, motor mount, trans mount, leaf spring and shackle bolts, u-bolts, transmission/t-case adapter bolts, bell-housing bolts, hell, even have a look at your flexplate to converter bolts, if automatic. If it's all been apart recently, that's an even better idea. Anything you've rebuilt, changed out or repaired.
Actually drop your driveshafts to inspect your u-joints and actually pull the caps off the joints to look at the bearings and cross. Even if they are new.
The easiest answer to the pinion and tcase output not looking at each other, is a blown motor mount and/or trans mount and possibly leaf spring bushings. Or if you messed up a measurement while re-welding your perches. Worst case scenario is somthing bent.
If you've done all that stuff already, disregard of course. At that point, it's probably time to start lookin at internal parts.