The picture in Mike's post showing the pump coupling is incorrect.
All Majors from 1952 to 1964 are on Number 1 cylinder when the coupling clamp bolt is below the drive shaft. If your timing marks line up with the coupling clamp bolt in that position you are 180 degrees out.
This picture is taken from the Fordson Tractor Workshop Manual. A rule of thumb we used when removing pumps:
Before removing the pump always check the position of this clamp bolt. If you do this and then put the pump back on with the marks lined up you will always be right.