Couple of questions on sheetmetal/bodywork

Is that quarter permanently welded in yet? Or just temporarily tacked?

First off I am NOT a body man and these are just my opinions or observations.

So...looking at the pictures.
First, I would make sure the door hinges are perfect with zero slop. You can get a rebuild kit with new pins and bushings. No sense making things even with worn parts involved.

If you put a thin shim between the upper hinge and door, that would lower the top of the door at the quarter and help to even up the bottom vertical gap where the door edge meets the quarter. But the bottom gap would be reduced. If the front was tacked and the rest was free to move I'd be tempted to put a hunk of 2x4 against the panel at the latch area and drive it back about a eighth inch or so, then tack the rest of the panel to hold it. Do not do any final welding until it's as good as you can get it.

AMD are reproduction parts made from new tooling but they may be off a little and not fit every single car out there. You may have to compromise everywhere so the differences are not as abrupt and even things up with welding in filler material or plastic body filler. Lokk at the interiuor of the door and see if it has been pushed in during it's life and filled with bondo to cover the crease. That would cause the door to grow vertically.

It looks like the straight edge on the new panel where the side of the panel meets the short concave panel under the window needs to be "adjusted". Again, with me not knowing much I would consider making a bar maybe 3" wide by 1/8" thick with one of the 3" edges rounded over. I I don't know maybe 10-12" long. I would hold the rounded edge against the inside of that crease and use a hammer on the other end of the bar to drive that crease upwards. Not too hard, just bump-bump-bump to get that edge higher with a little sharper angle between the two surfaces. It still would probably need some filler but not as thick as what is needed now. I may be all wet but that's what I would try. Good luck!