Such an amount of what seems to be rust must be coming from the tank. I've seen hard fuel lines spit out a lot of rusty gunk before, but hardly enough to clog filters more than one or twice before it passes.
Twice in my life, I have dealt with rusty automobile tanks. Both times, an Eastwood product solved the problem permanently. They were both gas cars, though. I have no idea if the same product is suitable for diesel tanks, but I suspect it might be. This is the stuff I used:
http://www.eastwoodco.com/shopping/product/detailmain.jsp?itemType=PRODUCT&RS=1&itemID=382&keyword=10165z
But holy cow, it didn't cost so much back then. Darned inflation!