Early A Body Fender/Engine Compartment Alignment?
On 65 A-bodies you have a pin in the front hole, the lower hole close to the rockers and the rear upper hole close to the door. Reason is to help the assembly line workers to hang up a fender and then focus on getting them in line. Usually you have shims in all three locations.
You should have a rubberised body sealer between the body and the fender. It was on a roll and simetimes added very strange.