Hello.
The way that I do it is to line the door up with the rear quarter panel with the front fender off of the car, leaving a gap of about 1/8 inch between the back side of the door and the front of the rear quarter panel, and then fit the fender onto the car and try to have about a 1/4 inch or less for a gap between the front fender and the front of the door. Sometimes you can get it perfect, sometimes you can't, depending on whether or not the front fender is a Ford piece or a cheap repop, whether or not the door has been re-skinned, etc... These cars were a far cry from perfect when they were brand new, though.
1965 door to front quarter panel gap 
