So here's what I found:
The areas marked in red with the Xs through them are the 3 areas where the floor has rusted through. The biggest hole wouldn't fit a quarter, but the metal is thin and has been weakened. These are the areas that I have to replace. The blue areas are sections of the floor where the metal is still thick and sound, but the rust has penetrated below the surface--this area is pitted. While I could get by with cleaning up this area then using a product like POR-15 (or something newer) I'm going to go ahead and cut it out. The other areas that show up rusty-colored are just a light coating of surface rust. This will be easily removed using mechanical means, such as sanding or media blasting. I'm surprised that the rear foot wells were only surface rusted--they look as if they'd gather a lot of moisture.
I did find that it got a bit hot when sitting in the car with a heat gun and a putty knife removing the old "soundproofing." So every so often I'd stop to cool off, and work on another part of the car (when I didn't run inside and get a drink and watch some football--this is a hobby after all, not a job!) So I removed the side rear window assembly, the outside rear view mirror, and the wing vent. All the glass needs to come out of the car anyway, so I got a head start on it.