Just a quick thought....if you are going thru the expense and trouble of stainless panels why not go spend a bit more and put on a new body?
How bad is the current body? Will (if any is there) the body rot just get worse? In the future will you lk back and wish you had changed the body?
You are going as far as putting a 350 in her so this sounds like a serious project. I think you have the right idea trying to plan out the project in advance.
It seems when you start building a Jeep w/o knowing exactly what you are going to do it: A. seems endless and B. goes in multiple directions.
Now.....how about those rears????