Have you checked your rear axle pinion angle? It needs to be the same angle as the engine and tranny.
I have always set my pinion angle at a -2 degrees with full suspension load. This is to compensate for the rapping of the different underload.
A problem I had back several years ago on my 69 when I installed a new clutch and had the flywheel resurfaced. Once installed I had a vibration in the shifter above 3k and got worse the higher the rpm to the point it would shake the whole car. Swapped out for another clutch and same thing. Pulled it out again and swapped flywheels and vibration gone. Moral of the story is make sure the flywheel & clutch assembly is balanced.