First thing, did you have the hardened stator put in when you had the tranny rebuilt? I'm thinking maybe the splines on the stator are worn and the torque converter is slopping around and shaking the crank into the thrust bearing.
Does it seem to be shifting OK? Is it staying in gear and overdrive?
It could be a broken pump vein or ring, bushing or about 1000 other things in there, you need a pressure check, but if it is shifting and other wise normal I would suspect a worn stator.
Keep us updated with any new info.
Mike