I guess great minds think a like, because that is essentially what I did yesterday. So my output flange is out 9.5 degrees not 5.5 (which is for sure the problem). So I raised the Tcase 1 inch with a jack, and got 0.5 degrees. I then took the motor out off the mounts with the hoist, and lowered it 1 inch (I only have 1.5-1.75" to play with), and got another 0.5 degrees.
That gets me to 8.5 degrees which is still a long way from where I need to be.
I ran out of time, but I am really at a loss for how the angle can be so different. What I mean is, the engine cannot really be much lower, the Tcase is at the exact same height as stock (just clocked). I would have to lower the engine a foot to get close to level.