So as I run this thru my head, the angle from Tcase to carrier bearing shouldnt be giving you any vibration. That pillow block is mounted solid and the ujoints don't know the difference- thats what they do. In your overhead pic, what's the angle of the driveshaft from the pinion to block yoke on the frame? Raising that block is gonna mess with the angle to the front yoke, which is what you're trying to equal out. Not sure thats the answer. "Clocking it" may be the better way, IF you have to go back into it that far. I still think your problem is in the slip itself. I'm not arguing with what Woods said, but I guess if it were me, I would have them lengthen it first.
I've got a very similar situtation going on, and Ive sat and stared, drawn, measured, cussed, and started measuring again here.... lol