After getting mine clean, I did the Ospho on mine, sopped up excess let it dry overnight per the instructions. The a thick double coat of black POR15. Dry between coats.
I later learned from actual pallet and body guys that it’s better to do the epoxy primer Master Series stuff. But my welder put POR15 over welding primer on a new floor board and riser so I just did the same in the other side. I still think it’s going to be sealed for years to come. Just don’t forget to replace your seam sealer topside and underneath in the factory locations.
Another vote for a rust converter (I use Picklex20) followed by Mastercoat Master Series silver. If you wanted to "smooth out" the pits you could squeege in some 2-part polyester glaze before your top coat.
I believe master series silver has a thicker product (master extreme) for pits. You spread it on and then scrape it flat. You then Follow that application with a coat of MSS. A second option is that You could put one coat of MSS, bondo coat, and then add another coat of MSS.
Treat it with PA (milkstone remover at your local farm and feed is way cheaper than most "automotive" acids and is the same thing) then a couple coats of master series. You can let the master series separate out and use the thicker stuff from the bottom of the can to fill small holes and pits.
I’ve used both SPI epoxy and MSS during my restoration, and both have been very good. I’ve been gravitating more to MSS, especially for the frame/rockers/torque box. I really like that I can use phosphoric acid to convert the rust, but this also protects it for a length of time as I might not be able to coat it with MSS right away. With epoxy, you usually can’t coat with PA (depending on the epoxy) unless you neutralize the PA before epoxy primer. I would rather not worry about whether or not I correctly neutralized it. And if you take the metal to bare metal, you would want to protect it quickly, whether it be epoxy, PA, MSS, etc.
The MSS is really easy to apply with a foam roller and looks nice, but honestly who cares what it looks like because it will all be covered. Using the foam roller is a little easier and cleaner than using the paint gun, and there’s no overspray. Epoxy also works best with clean bare metal. Phosphoric acid then MSS would work well on your mildly pitted floor.