This is a hard one. Mustang panels never lined up very well from the factory.
The rule of thumb is to start at the back of a car and work forward.
First question - did you rebuild the hinges? If the hinge pins are worn, every time you make an adjustment it will change when you close the door.
Here is how i used to do it.
Firstly, remove the lock striker plate from the door jamb. These are for the locking only and should not be used to support the door.
Fit the hinges to the door, using the old marks around the hinges so that they are in the correct location.
Place some shims/ packers about 4-5mm on the rocker panel where the door will sit. Will help to support the door and provide the correct gap.
Place the door in position with the aid of a helper. Locate the hinge studs through the side panel and fit the nuts, but not too tightly. Swear and curse as you adjust the door hinges to obtain about an even 4mm gap where the door meets the rear quarter panel, and about the same gap at the bottom of the door. Once you are happy with both gaps tighten the nuts.
Note at the above stage the front guard should not be on the car.
Next, adjust the in/out position of the door by loosening the bolts where the hinge meets the door. Adjust in or out as required and retighten bolts.
Refit the striker plate after all door adjustments are done, then adjust striker plate for smooth operation of lock - ensuring that striker plate is not supporting the door.
Hope this helps.
Rocket.
