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.