A shackle lift still effects the drivline angle, any change in suspension (ride height) changes this angle... A body lift would have no effect. All of that aside, I agree that a shakle lift shouldn't be causing this issue, especially all at once.
The usual start is going to be the driveshaft ujoints. You'll need to chuck the tires, place the heep in neutral, and crawl under to check the drive shaft for forward and aft play, as well as side to side play. Any play at all, especially near the pinion, would point towards a failing ujoint.
If you have an SYE you can remove the rear drive shaft, drive the heep in 4wd and see if there is a difference. This will allow you to eliminate rear ujoints as the problem entirely.
Vibrations can also come from the front axle shaft ujoints, the are somewhat harder to inspect. I'm sure some of our more tenured folks will be in here soon to offer adtl advise.