Normally that vibration comes because the angle between the rear shaft (cardan) and the rear pinion is not the same as the tail of the output shaft comming from the transfer and the same rear shaft (cardan)... when you lift the rear suspension you must change the angle... it can be corrected changing the angle of the rear differential pointing up or down to the rear shaft keeping the same angle of the transfer output shaft and the rear shaft.

Small vibes will kill you your u-joints badly...

JorgeA