Great, Megatron! Your truck deserves to be free of shudders...
When the U-joint angles are different, opposing joint rotational forces work against each other. Envision the angled arc that each U-joint follows as it rotates. Since part of the joint "compresses" and the opposite side "expands" during each rotation, there is actually a speed-up and slow down over the arcs. The driveshaft/joint input and output speeds remain the same; the U-joint design compensates for speed variations during each rotation of the joint.
Simply put, if the rear driveshaft's front U-joint angle differs from the rear U-joint angle, even if the two joints align properly in "phase", they have irregular speed-up/slow down patterns over their arcs of travel. So you get a vibration because the shaft is fighting itself end to end. Another cause for this vibration is when a splined driveshaft is assembled with the cross-joints misaligned. This is "out of phase" and a real cause of vibration. It can even tear apart the driveshaft since the speed-up and slow down over the U-joint arcs of travel run at different cycles.
You mention power/torque, and that brings up another concern. A driveshaft loses torque capacity as the angle/slope of the shaft increases. When a vehicle gets "lifted", the typical 4x4 scenario, if the driveshaft slope increases, the torque capacity of that driveshaft diminishes. U-joint life suffers, and failure of joints is often common. Even when the U-joint angles match as they should (by shimming the pinion angle or mid-shaft bearing properly), the U-joint lifespan is shortened. This is strictly a function of U-joints: steeper angles make the joint weaker.
One way many offset this risk is the use of a CV or double-Cardan joint at the transfer case output yoke and a single Cardan joint at the rear axle pinion yoke. The CV not only reduces the angle on each joint within the CV assembly, it also helps knock off the driveline slope factor considerably. Since the double-Cardan CV joint has "self-cancelling" angles between the two cross joints, the rear axle joint angle (a single Cardan cross joint) can be very close to straight when measured at static vehicle height—with axles weighted or on the ground.
Actually, 0-degrees of U-joint angle is unacceptable for U-joint survival. When running a CV driveshaft, I set the rear axle pinion joint (single-Cardan) for 1.5- to 2-degrees angle with the vehicle at static curb height and weighted. This minor angle allows the joint's needle bearings to rotate in the bearing caps, which prevents them from starving for lube and also distributes the load uniformly over the needle bearing sets within the U-joint caps.
Note: The 1.5- to 2.0 degree rear joint angle is achieved by rotating the axle housing to angle the pinion shaft and yoke upward. There is only one "downside" to doing this: Lubrication/fill of the differential is thwarted by the dropped fill plug height. Aftermarket differential covers for lifted trucks often have a relocated fill plug, higher on the cover to permit normal fill levels with the pinion angle rotated.
The amount of rear axle rotation has little affect on chassis geometry or spring action. Many lift kits provide a tilting spacer block to restore U-joint angles. On installations that require use of spring-to-perch wedges to restore the rear U-joint angle, I use steel and not aluminum wedges. Steel will withstand more punishment and not pound out or loosen over time.
Thanks for letting us know how this worked out, Megatron! Great to hear your Ram is back in top form...