I just completed putting two half pans into my car. Basically, all four foot wells were rusted through. I installed the entire half pan on the drivers side, and just the footwell areas on the passenger side--leaving the areas under the seat mount and under the rear seat because it was good sound metal.
My personal opinion is that you would be absolutely crazy to replace the entire floor pan if you only have rust in one footwell. That sounds like one heck of a big job to me. Also, I believe that if the original metal is still sound, it's in the best interest of the car to leave it there. The original metal seemed to be a bit thicker than the floor pans I got from Classic as well.
If the car were mine I would buy a partial pan that will cover the hole, cut out ALL the rusted area taking a bit of good metal around the outside of the hole, cut the patch to the proper size and weld it in. After grinding the weld down flush I would put on a brushable seem sealer around the perimeter of the repair.
I'm a long way from being any kind of a body man, but this is how I would proceed.
