Exactly how is the pinion angle set... or at least what was your goal when you were adjusting its angle via the cam bolts? Most of the time, especially with a TJ, you will have vibes with a 3.5" lift if you only drop the t-case an inch, no matter what you try to set the rear pinion angle to.
I'm now even more convinced you have an angle problem that MAY be reduced enough to get rid of the vibes if you add a pair of 1" taller motor mounts. The 1" taller motor mounts add to the effect done by the 1" t-case drop.
But again, what pinion angle were you shooting for when you were adjusting the cam bolts? Were you trying to get the pinion angle parallel to the t-case output shaft?