I'm thinking it's got to be driveshaft related. You're essentially running a 3.5" lift because of the belly up. It raises the transfer case even higher than the 2.5" from the OME. It's probably from the driveshaft operating at higher angles.
You might also want to check your pinion angle. It's supposed to be 1 degree less than the driveshaft angle. I forget which is which, but if it's too high, you'll get vibrations during acceleration and if it's too low it will vibe during deceleration.....or vice-versa, I can't recall.
Either way, checking the pinion angle and looking into a CV shaft would be the first things I'd do.