I'm going through a similar effort as you right now. I've done some metal patchwork here-and-there before. But, never as much as I'm doing on this truck. Basically, replacing lower cowl, door pillar, kick panels and rocker panels. Looking for a respectable appearance but not show quality.
While I'm not completely disassembling everything at once as in Kevin's (very excellent) pictures, I am doing one side at a time. It would be great to have the space, time and resources required to yank the cab and do the work off the frame. I just don't have that type of setup. Plus, it helps to reference the other side if something unexpected comes up. And, I know I don't work very fast or have that long of an attention span. So, my intent is to work on a different portion each winter and drive the truck in the warmer months.
Here are some things I've found (with repeats of comments above) getting this (almost) done.
While I can't control what's rotted out and no longer there, I do try to limit the amount of metal I cut out to only what's rusted to get to good metal. For example, rather than replace the entire floorboard or outer cowl, I bought replacement panels and chop them up to make the necessary patches. In my case, some things had to be completely replaced (rocker panel). Limiting the amount of removed metal, I think, helps keep things in place with minimal bracing required. I know this isn't always possible. But, from your picture, it looks like you wouldn't have to replace the entire floor. Well, unless you want to!
As per the above, before cutting things up, try to get measurements or make braces or jigs to help line things up later. For example, I had to replace the lower door pillar to a point just above the hinge. Before removing that section, I drilled two plates to match the hinge mounting and welded a bar between them. When it came time to weld in the new patch panel/hinge, I bolted that jig between the top hinge and the patch panel hinge to make sure the orientation was correct. Made replacement easy. Of course, this only works if you have a place to start. I'm interested to see how the parking brake braces and hardware line up when it's done. All of that was rusted out with no way to get measurements before starting.
Next, unless you're using NOS panels/sheetmetal, not much is going to line up perfectly. This has been mentioned on this board a number of times. I couldn't agree more! One of the things I've tried doing that relates to your "where do I start" question is to prioritize mounting points and body lines. Then, work from there. I mentioned replacing the lower door pillar. Most important thing was to get the hinge mounting perfect. When I did that, I had to "tweak" the door pillar-to-rocker panel area. The other important area is the outer cowl. Getting the hood/door/fender gaps and fender mounting right is most important. If I need to "tweak" the hidden pieces between the outer cowl and kick panel, that's what I'll do.
My specific sequence was : rocker panel, floorboard, door pillar, outer cowl, kick panel, inner cowl. This made sense since I didn't need to replace too much of the floorboard. From your picture, I might have done the floorboard before the rocker panel? Like the outer and inner cowl pieces, there's a lot of contact between the two that can limit how far you can move things before you have to cut/weld to get things to fit.
Finally, keep references like Kevin's pictures at hand. I really wish I'd have seen those before I started. Really helps to see how things are supposed to go together. Manuals and drawings are good to have. But, there's something about an actual picture during step-by-step replacement that really helps me understand how things go together.
