Stats: 95 f250 7.3l reg cab 4x std, rebuilt 5 spd last year, installed new leafs for a 3" lift this year.

I've owned this truck for 3 years now and it has always had an appetite for ujoints. I'm am now quite aware of the oncomming crap out of a ujoint to say the least.
I'm looking for confirmation of things I think I already know.
The front end seems fine everything unlocks and frees up, I can turn the front shaft and there is no engagement to the front hubs.
The rear end is the problem.
the good: new slip yoke, end yoke, and pinion flange, shaft has been balanced
the bad: shackle bushings were not replaced some slop evident

Heres the problem: Its fine up until 100kph/60mph then I get a vibration set up. I can feel it in the pedal and see it in the steering wheel not to mention the noise its making.
My conclusion is it is out of line some where. I have checed the diff angle with a magnetic angle finder and although not the best tool things looked to be within tolerance.
My questions: could it be the transmission
could the trans be out on the horizontal, there doesn't seem to be much in the way of adjustment.
could it be the diff, when I replaced the pinion flange the pinion gear was sloppy until I pounded the new flange on. I've had it apart before to do the lts slip clutches and things looked ok then. There does seem to be some excess "lash"? in it.
My thoughts on the fix: I can borrow one of those hilti laser levels and try to find the diff angle and see if they are out of line then adjust from there.
Any thoughts?

 

if everything is good sounds like your crushing the new joints.tightening the caps too much eggs them ,and needle bearings dont work, and joint becomes junked from not properly working.