While poking around the rear one time, I noticed there was a soft spot in a corner. I pulled up the carpet a little and saw a big rust hole underneath. I decided to remove the carpet completely and apply some bedliner in the rear. After comparing several different brands, I decided on Durabak. The main reasons I went with Durabak was their selection of colors and ease of application. I ordered a gallon and two quarts of brick red to match the rest of the interior color. Since I didn't know how to weld, I decided to fix the hole with a patch panel attached with a combination of rivets and epoxy.
This is what the rear looks like after pulling the carpet out and removing the side panels. I left the seat mounting points and the metal rails on the side because I couldn't remove the bolts and screws due to the rust.
This is a closer view of the left side. Notice the rust that has formed near the edge of the floor where it meets the tailgate. Years of water leaking through the rust holes of my old tailgate caused the edge to rust.
This is what the hole on the right side looked like after I cut out most of the rusted metal. The previous owner had an internal tire carrier before installing an exterior one and it seems the bolts used were a different metal and the incompatibility of the floor sheet metal and the bolts caused the rust to accelerate in one area. For those of you who have an internal tire carrier or had one before, I recommend checking under the carpet around the lower rear mounting bolt for any rust.
I coated all the rusted areas with Corroless rust stabilizer from Eastwood. I've heard that Corroless does a very good job with rust control so I ordered a pint and it seems to be pretty durable.
This is what my patch panel (18 gauge) looks like after riveting and epoxy around the edge. The epoxy I used was PoxyWeld I found at Menards. It hardened in less than a half hour and was pretty decent to work with. After it all hardened, it is more solid than the rest of the floor since the original sheet metal seems to be around 22 gauge.