Well all that rust in the system is never good for injectors.
But did it get to the injectors?
Rust was found in the fuel bowl and tank filters.
Since the Fuel return line is at the bowl, this indicates the rust, or at least the rust that I've found, was generated in either the feed line TO the bowl, or return line FROM the bowl. The fuel filter in the bowl *should* have stopped any rust from entering the rails in the heads, HOWEVER, that does not mean that the rails (in the heads) are not rusty as well. It makes perfect sense that rust in one section of the system would mean rust everwhere....
Although I do not know if rust can form IN diesel fuel. It does not form in gasoline, you must have no fuel in the lines for rust to form in a gasoline system.
I'm assuming the rust formed while the truck was sitting at the dealership waiting to be sold, with low fuel in the tank.
Of course, if rust CAN form in un-treated diesel, that throws that out the window, and then I should assume the internal rails in the heads are just as rusty as the rest of the fuel system. In which case the injectors might even be rusty.