I would take out the rear portion of the floor before cutting the long load path to adjust door gap. This is assuming that you are going to have to replace a portion of the floor to fix the bulkhead rust damage.
The more material you take out, you’ll be amazed at how it softens up the chassis and lets the turnbuckle door braces move things.
The other thing is the chassis will be stronger if you don’t have two structural panels just being joined by a butt weld. The other thing is the need to account for metal shrink as weld cools. I.e., if you set the door gap perfect, then do the butt weld to rejoin what you’ve cut, you’ll find the gap tightens as the weld cools.
The other thing is that when you start welding in rear bulkhead pieces, you’ll find that weld shrink pulls the long toward the center. That pull may help your door gap situation. The whole chassis will have moved around as the structure rusted and lost stiffness over the years.
The other thing is that on my car, I found part of the lower rear door gap was controlled by the door jamb sill. I had a bit of a fiasco that needs to be repaired in the future because I was holding that gap with silicon bronze and then it moved when I overheated things allowing the silicon bronze to reflow and my gap moved.
Some of this would vary depending on order to remove or install. In unibody construction the parts are all inner related. It’s sort of trial and error, learn as you go - at least it was in my case.
My advice is don’t try to set door gap too early. Keep an eye on it as you do other work. Keep it close to what you want but don’t sweat it too early before you get an idea of how other work moves it around