The crossmember with the angled area for engine mounts is for a 1954 or later frame. It is used with a different bellhousing than the one with the vertical mounts in your picture. Somewhere along the way there has been a mismatch between the crossmember, the bellhousing, and the motor mounts. It looks like someone has modified the crossmember to use the earlier mounts, and probably drilled the holes a little off position. That will result in some misalignment between the transmission and the torque tube, and possibly a vibration problem.
Jerry