Looking at that rear driveshaft, I would suspect that most of your vibrations are from it!
Rule #1 in driveline design is "Make the flanges Parallel!".
Tilting your rear dif up as indicated in the above picture causes the U-joints to operate out of phase with each other causing vibration and wear.
See
http://www.4x4wire.com/toyota/tech/driveline/and
http://www.4xshaft.com/driveline101.htmlFor a detailed explanation.
Exception to Rule #1: If you use a Double-Cardan driveshaft, you
may point the differential flange at the transfer case output
if you put the Double Cardan joint at the transfer case end.
See the above links for detailed info on Double Cardan setups.
I get the biggest laugh out of older, wildly-lifted pickup trucks that have regular driveshafts and the differentials pointed at the transfer case. It's odd - I mostly see them at the Auto Parts store...