I think it is in your best interest to keep as much original metal as possible. See what things look like after you get to it with a sand blaster or wire wheel. If you only have a few small sections that are bad, I'd just cut out patches from the new panel. Is that car factory AC? Reason I ask, it seems only the passenger floor is bad.
In my case, my car was factory AC. The driver's side floor was mint, and the passenger floor was horrible. I had to do a full passenger pan, front to back. You are probably also aware, but the reason the floors rot out is the rusted cowl vents/hat. You will probably need a plan to address that at some point.