The centreline of the pinion should be parallel to the centreline of the transfer case so that both UJs operate at equal angles. If you point the pinion at the transfer case it will make it worse. 4" lift is about as much as you can get away with without a t/c drop or motor mount lift so it has to be set up pretty well to eliminate those nasty vibrations.
If it has been ok so far, something must have changed. As already mentioned, Take the rear prop off and check the joints for wear and tightness. If you're sure it's ok, check the front one as well. If they're both ok, in fact before you even check that, check the U-bolts holding the axle to the springs are still FT, If the axle is moving about it will cause vibration. It's also worth checking the bushing in the rear of the transfer case isn't very worn (does the slip yoke have a lot of up and down movement) or the transmission mounting hasn't turned to mush.
