LETS COME BACK TO THIS EXCELLENT SUGGESTION. Assuming the door is OK, align it to the quarter panel and rocker panel. This is ALWAYS the way you reassemble and align everything. The doors have to be fitting against the quarter panel and rocker first. Then align the fenders. You may still have to tweak the doors a tiny bit, but if they are nicely aligned against the quarter panel and rocker, you are 90% there. If the door is properly aligned and you still have that gap, it is time to 'make' it fit. You will be doing some cutting and welding. You might even be able to fix the gap by adding a bit to the door. Either way, it should not take too long. It's hard to tell without seeing it.
