KBrown, I was in the same boat as you with my '57 cab being in very poor condition starting off. I've replaced most of the floor, both steps, front inner and outer corner, rear inner and outer corners, all three of the cowl panels (I believe that is what you are revering to with the airbox corners), and I have the same problem areas with the roof as well.
My advise is to start with the floor that way you will first off gain some experience cutting and welding patch panels in an area where it is fairly easy to hide mistakes. Then move up from there. I did both of the toe boards, then steps, front corners, rear corners, cowl panels and fire wall, and will be starting the roof soon. My plan is to cut off and replace both the inner and outer roof panels. You said you are going to try and re-use the outer roof panel, while that it always a novel idea, you might want to plan on a new one. Being that when cutting the outer off, from experience panels like that never just detach themselves willingly or in a pretty manor to where you can just easily plop it back on when you are done. The roof panel is welded on by a couple hundred spot welds, undoing all of those is going to be a P.I.T.A.
Also, being that your floor is in bad shape, your roof is actually the most structurally sound piece at the moment keeping the whole top half of the cab square, so leave it until last. It looks like your cab is still mounted to the frame. IMO put some bracing across the bottom half of the cab, unbolt it from the frame and work on the floor. As long as you do not go crazy cutting up the floor it is unlikely that it will get out of square. Just work in one area at a time and it'll be fine.
