Then only place to measure the tranny angle is the tail shaft. Likewise the only place is the pinion yoke for the rearend.
You are correct the trans must be tipped up (positive), rearend tipped down (negative).
I set mine so they are as close to same angel (-/+) so the tranny and the rearend are parallel.
Sounds like you have a bum transmissiom mount.
I had to shim both to get it correct.