I always go on this. If I feel it in my feet is front end and if I feel it in seat it's in the rear. (Yes does sound stupid but WHATEVER.
TT, when you lift a TJ/YJ with the stock shaft it pulls out of the slip yoke some. This also puts your ujoints on a different plane then they were used to. Hence the vibrations. You've combatted this with a bit of a TCase drop and a BL/MML, but as you wheel it and things hit on other things. You can easily out of balance your driveshafts which tends to throw all that work out that you did to get rid of the vibes.