Are the door hinges original or pattern?? I have had issues with pattern hinges being slightly thicker than the originals.
Now if they are original you could try and skim some material off the mating faces of the hinges but looking at your pictures your window frame will hit the front of the door aperture.
Now although i would not advocate this you could section the quarter panel to dress it back to open the gap there.
So this is my lads car which fought me every which way you could think off. I should have seriously cut my losses with this one but we carried on. So the same side as yours with a very similar issue although my A panel had not been fitted. I also made the rookie error of fitting my panels in the wrong sequence but certainly learnt my lesson from this car.
So gapping issues like yours certainly at the rear of the door.
Marked out where i needed to section.
Sectioned and dressed back the affected area then tacked.
And the final result
This was a lot of work plus a lot more to do as well but it fitted so much better. Wahtever you do if you go down this route try a get £1 gaps as a minimum, DO NOT go tighter.
