I'm kind of leaning toward what some of the others have mentioned- using 2 tanks to keep the 2 different types of fuel separate. Use one tank for "clean" fuel- diesel, clean gasoline, etc. The the 2nd tank for "mystery fluids", all the stuff that could have any contaminants in it, or could gel more easily.
In keeping with your redundant systems, I would have separate fuel systems all the way to just before the injection pump. Each tank would have its own course primary filter, then a secondary medium filter, and last, the fine filter.
To add to the system, the "dirty fuel tank" could have it's own cleaning system. Install a 2nd fuel pickup, pump, and filters that are only for circulating the fuel from the tank, through the filters, and back into the tank. If you get a batch of something you want to make extra sure is clean (used motor oil, used veggie oil) pour it in the tank, flip a switch, and let it circulate and clean for a couple hours while you run on diesel (or are parked) and you'll be surprised at how clean it will get. Using a dedicated pre-filtration system will help keep your main filters cleaner, with less chance of downtime on the road due to an unexpected dirty filter. It would be extra plumbing and parts, but the extra cleaning would be well worth it. You should be able to fit the pump and filters right next to the tank, keeping everything fairly compact.
Just a few thoughts...
Jim