All those parts/pieces are structural but if you've got an opening at the bottom rear portion of the door, it's the door doing the sagging.
The 'A' pillar holds the door hinges in alignment and if it's junk on the bottom, it's moving.
With the top off, your firewall is moving, that's why when you put the hard top back on, everything comes back into place.
Post some pics, let us see what's going on if you can.
How are your skillz?
You ready to tear into this?
Here's a couple pics of how well these old trucks hide the rust.
The lower 'A' pillar
LOOKS okay in the first pic but not so much once the outer rocker is pulled off.