I have been chasing the same problem for years. At speeds below 30, while accelerating, there is a slight shaking. It is the same regardless of throttle, so it is not axle wrap. I have set the pinion at different angles and the problem changes, but never goes away. It just isn't bad enough that I have made the move to the real solution: CV driveshaft. I believe the real problem to be the inherent play in the slip yoke and T-case to cross-member mount. I think this prevents the forces at the two U-joints from completely cancelling out. I think that a fixed yoke T-case could also help, and to a lesser extent a brand new slip yoke.
I have had "wrong" U-joint angles before and that caused vibrations at pretty much every speed.
I hope your problem turns out to be simpler. Check the U-joints and U-joint angles. An angle finder is cheap. Some people fix it real quickly by lowering the T-case, if you're not opposed to that.