I am not sure.. possible it was bent? Maybe the door was pushed down a while ago.. Also look at where the hinges are mounted on the door and body, possibly you could adjust them to raise the door a little. Not sure if you mentioned you had a service manual for the door? I could send the measurements if you would like. About the door lock. That only made my doors loose since they would move around but still stay shut.
I would try adjusting them up to see if it is maybe that someone had taken them off and put them on wrong.
If you would like I can send pictures of my doors and hinges. Or you could send me some at email@example.com so I can maybe see your problem?
Did anyone ever have the doors off this car for a long time? Because the frame and body could’ve gotten bent which might cause the doors to not shut properly.