I had a couple problems with my convertible to after I removed the door lock mechanism that mounts to the body of the car, aparently there is a small weld on that piece and it does not come out of the car (easily at least). If you knock the lock around or tap the piece with the weld it will break loose and move around, not properly lining up. Also make sure if you have a service manual to check the measurements of space needed to seperate the bottom of the body from the bottom of the door. Also your hinges may have been put on lower then needed. Make sure they are not damaged or bent.
I do have some doors and parts for sale if you need replacement parts.
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 firstname.lastname@example.org 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.