My issue isn't with the body line lining up, I'm just going to live with that, the issue is really highlighted in the second picture. That big dark gap isn't an optical illusion, it's literally how much the contour of the body (right beneath the body line) sticks out and doesn't match the contour of the cab. You can see the rest of the door lies flat with the plan of the cab.
It almost seems like I need to slice open the edge of the door skin and massage that contour in so it lines up better, and then reweld it.
If the door is in the right place, slice it, line it up and re-weld.