Stuart
If this is the original '69 Ford shifter, check the alignment as mentioned. I had to make up a 1/4" rod with a 90 degree bend in the end, of just the right length, to be able to insert it into the alignment holes. Clearance is tight between the shifter and the side of the tunnel.
Remove or loosen the linkage at the shifter, insert the alignment tool, and then re-attach the linkage. This process is more awkward if you have a lower boot installed.