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I am currently trying to adjust my doors BEFORE installing the door seals. My question is at the bottom of the door does it set in, set out of is it just flush with the rocker panel in a 1966?
I'm not sure of the bottom door alignment but have a couple of tips since I have done his job several times.
I usually take the door striker off the truck so it does not interfere with aligning the door. Get the door where you want it and then align the striker to the door.
I have also found it easier to install new door seals with the door completely off the truck. Maybe I'm just too lazy or too old for the contortions necessary to get the seal seated properly. It is much easier if the door is on a bench. It also makes it easier to clean the seal mounting surface.
To be honest, I haven't looked at my '65 closely but most trucks of this vintage had some way to adjust the window bows in relation to the door.