At what MPH range are you getting vibrations? I just put in a JY shaft myself (from a JZ) and adjusted the pinion angle the best I could (eyeballing it). It kinda has some noise at lower speeds but when you get going they seem to go away.
01 WJ Spec. App. Laredo. Retrofitted with Akebono calipers; Stillen Sport Rotors; Reese Class III Hitch; and a ZJ Front Drive Shaft
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Utah Jeep Crew #8
FS: Rear wind deflectors || || Stock OEM Air Box Set Up