Do you plan on processing the fuel yourself, or buying from the pump? I make my own fuel, and with the money I have in my setup my truck and the next few will be long gone before it pays for itself with as little I make. If you are making it, do yourself a favor and spend alot of money on wash systems and dryers, filters and scrubbers. I have had my fuel ASTM tested a few times and passed with flying colors thanks to my new polisher system, but it cost me a few grand. Making fuel is just a hobby of mine. I dont intend to save money, I do it for fun with my father.
Being your truck has lower miles, I dont think you will have much buildup of deposits in your fuel system. I'd just fill her up and stay with 10k filter change intervals like normal. But for the 12v, I'd change filters about every 3-4k miles, if not sooner if the truck starts to lose a little power. And your right, those 12 valves will run on anything!
One other thing I would recommend is if you do the aftermarket lower micron fuel filter, I would switch all the rubber hose to Viton. It takes a while for biodiesel to degrade the factory rubber lines, but it will. It will eat it from the inside out, and will only swell the line when it is about to blow. Its pretty expensive hose, I believe $6-$7 a foot.