I'll get pix showing the slight nose out of joint later.It's one of those tasks that seems worse than it is, kind of like the first time you pull an engine. Replacing the bushings and hinge pin can be tricky though, especially without a vice, but Vice Grips work to clamp the hinge to something so you can drill the hole to accept a new bushing. It's not complicated, just frustrating at times.
Adjustment may be repetitive and it helps if you only loosen the bolts just barely enough to let things move with slight persuasion. Put tape on the edges or faces of anything you don't want to accidentally scratch or chip- door and fender edges are prime places. You may need to buy new door strikers as well, as they tend to wear flat on top. When setting door gaps adjust the striker position first to get the rear of the door to match the car, then work your way forward. Take measurements of any gaps that are currently correct and you can match them later.
Do you have a picture or two of the damaged header panel?
My theory on the pin is that it didn't get completely rust-proofed/ painted and was corroding from day 1.
My plan of attack with the door hinge would be to replace it with the door closed. I have this fantasy in my head where I take the front driver fender off without losing the shims and replace the door hinge quickly.
I figure I'll sharpie witness marks and measure the current gaps like you said.
Variations on the theme have me supporting the weight of the door with a strap and cherry picker, with the door shut on the straps.