Driveline vibration!!! I need help!

Check the engine and transmission mounts, and what were the results of the pinion angle bit? What kind of exhaust is on the car and where are the hangers for it?
Rotating parts all create harmonics. Normally things are set up to limit that, but when you start changing parts, or moving them around, you can alter the frequency of them. If ti comes and goes, and doesn't do it when the drivetrain is loaded (either at cruise because power is being applied to maintain speed, or from accelerating or decelerating) it's shaking. I don't think it's tires or the shaft itself. I think it's the relationship between the angles that's doing it.