The difference may be caused by one tranny being floor shifted (downward pointing lever), the other column shifted.
I believe that removing the pan and loosening the large nut that holds the lever, you can rotate it to where it's wanted. However, if there's a difference in the length of the arm, this will create a different ratio. If this is the case, swapping out the arm would be the right move- if keeping the original shifter set-up.
B&M makes a kit to allow the use of a 3-speed B&M shifter w/the Ford AOD. It's P/N 40496