My rear YJ driveline vibration didn't go away until I did the following (2" OME lift):

1) removed transfer case drop kit; install slip yoke eliminator and CV rear drive shaft
2) have rear axle spring perches removed & rewelded for optimum rear pinion angle (off shelf shims weren't enough)
3) balance rear drive shaft; the shop that made it hadn't balanced it!

Vibration was finally gone. I have a friend with a 4" lift on his YJ, and he has no vibration. It musat have to do with the manufacturing tolerances of the rear axle.

Keith