I have a 99 Jeep TJ with a 3" susp. lift.  I was getting a vibe and figured out it was coming from the front driveshaft (no vibe with the front DS removed).  I replaced all of the u joints and centering yoke.  The vibe has drastically been reduced, but there is still a bit of a vibe there over 50 MPH.

I know that the rear pinion angle needs to be the same (or really close to) the driveshaft angle.  Does the front pinion angle need to be the same as the front DS angle as well?  

Any other ideas?  

Since front drive shaft has a double cardian joint by Tcase, you need to get angle as close to zero as possible at pinion end. If not possible, consider a after market CV up there. You might also have front shaft checked for balance.