Have you quartered the car? Are you going to?
If you are not then align your rear edge gap, leave the gaps a little larger than spec if the metal is bare.
I use gap spacers made from wooden dowels shaved to the correct thickness.
I tape them in place and usually leave the rear of the door about 3/16 high to compensate for weight of glass and regulators etc.
PERFECT GAPS require welding and filing.