Here's an update. Last night I just focused on measuring and correcting angles.
It took forever to get the yoke and pinion flanges at just the right angle to get accurate readings, but I got it pretty darn close.
1) Zero'd out my angle finder on the yoke off the t-case.
2) Then I squared it up on my driveshaft. 2.5 degree difference. (For your visualization, imagine the t-case pointed downwards 5 degrees. The driveshaft was half that at 2.5 degrees.)
3) using a deep socket on the cup of the u-joint in the pinion flange, I measured the pinion angle. 2.7 degrees.
This means my operating angles of the u-joints themselves are within spec, but they are not equal. On a one-piece driveshaft, the pinion angle should be parallel to the t-case/transmission yoke angle.
Rummaged around in my garage and found some 2 degree axle shims. With my impact I loosened the u-bolts and put my floor jack under the leaf pack with the help of a scrap 4x4 wood block. Created just enough separation to slide them inline with the pin. Dropped it down, tightened it back up, and torqued to 100 lb ft. Repeat the other side.
Results?
Zero'd the gauge on the t-case, measured the pinion angle - BOOM - only .7 degrees difference. This is actually ideal as the pinion will climb under torque.
Took her for a drive and the majority of the low speed vibes are gone! Highway is still there though. My shi* Goodyear LS2 tires aren't helping though even though I had them shaved.
Next I will put the overloads back in and remove the block and drive it for a few days to evaluate before using some leaf spring clamps.