Scott,
You can get replacements for those panels (and all the others) at K&K Manufacturing. I just replaced almost all of my floors with their panels.
Make sure you check the footwells where they bend up to the firewalls. The drain tubes from the fresh air vent tend to leak there and cause rust (ask me how I know). If the area is covered by the tar paper underlayment, you can check from under the car. While you're there check the wheel wells, particularly where they meet the rocker panels.
Pete S.