Dave,
I had the same problem you, Tom and Paul described, but I was never able to solve it. After thinking about now, I wonder if the cause is flexing of the frame. I did the engine and trans on my ’57 Eldorado using a two post lift picking the car up at the four wide pads on the X frame. This is only a WAG, but given the shape of the frame and cross member, the slightest bending would prevent the cross member from seating correctly. You might try finding and using a ramp type lift that picks the car up on its four wheels. Please post your results when you find something out.
HTH,
Ralph