When are you going to step up to Google Chrome as your default browser? All the cool kids are doing it.....
Typically, you should start with the structural stuff: frame rails, aprons, shock towers, etc. Sometimes, though, the rot is so bad that there's not anything good to attach these structural elements to. If that's the case, start where the metal is good, and work towards replacing those elements so that when you do install the structural stuff, it'll be solid. I'd keep the doors and export brace installed to help keep things in alignment. DO NOT remove everything all at once...do one piece at a time so you can maintain your alignment. You'll only have one easy shot at this...
John,Welcome to StangFix. We can provide engine compartment dimensions so you can ensure its all nice a square before you weld in your new pieces.