Are you telling us that the noise only happens when the clutch pedal is depressed?

Your new throwout bearing could be defective or the incorrect bearing.

The pressure generated by the clutch springs is moving something in the engine, transmission, or rear axle.. All of these components must have some sort of thrust bearings.

I had a '61 Mini that had worn thrust bearings that were so bad that you could see the damper on the crankshaft move, and eventually the engine would stall when the clutch pedal was depressed.

AS for testing with the rear wheels off the ground - is the noise exactly the same?

Since most of us do not run our cars with the rear wheels off the ground, we do not know what our car would sound like under those conditions.

I have a '64 544.