i have exactly the same issue. I have changed engine, gearbox, propshaft, differential, and cv joints, and the only thing that has changed is the intensity of the vibration and a slight change in the speed at which it occurs. I suspect it is due to propshaft angles being mismatched, causing a cyclic loading on the driveline. Play in different components such as UJs / diff / CVs does allow slack in the drivetrain at low load, so if you remove enough slack you may have removed the symptom, but maybe not the cause.
This is all a bit of conjecture as i have not yet fixed it, or been able to think of a straightforward method of measuring it. I was planning on changing the height of the engine mounts, as that's the only thing i think has changed in the approximate time period of the noise appearing.