I understand needing specifics from me to allow you to respond with specifics. Sorry for not being specific up front. I'm including a pic of the passenger side floor/inner cowl area as an example of what I'm trying to fix. The bottom of the outer cowl panel is rusted through, as well. There are similar issues on the driver side. One rocker has an elongated rust through hole, but most of it is intact.
I was trying to understand if it made a difference to do the floor first and index everything off of that or do the rocker panel and index off of that, etc. I'm guessing that the real answer is that there isn't an answer and each situation is unique.