If you do have as much rust as it sounds like, I'd highly recommend sand blasting before any work starts. It exposes all the problem areas and gives a fresh, clean surface to weld to.
A wire wheel is not enough prep for any rust, it needs to be mechanically or chemically stripped to bare metal, and a wire wheel will not mecanically remove enough. I really like file belting all seams and then preping with naval jelly or phosporic acid, then coating with a solid weld through primer. I run Upol UP0768 #2 copper primer on all sandwiched surfaces on reassembly. A spot weld cutter will be your best friend, the cheapo scamazon replaceable carbide ones work extremely well for the cost. Should be around $20 a kit for 10 of them. Saves a ton of time for all the spot welds you will need to be removing. Cleco Pins can also be handy for consistent mockup placement.
Measure all your door openings before you pull it off the frame for a baseline. It's pretty easy to get them out of square pulling rockers, quarters, and floors.
I make just about all of my panels besides rear sills, the CCOT ones fit okish, but the radius usually needs to be adjusted. If you have any plans for running larger tires, or flipping springs, now is the time to make those changes. I'd recommend deleting all holes you don't need, it gives a much cleaner overall finish to the build once it's done.