Water separators’ don't work well with the new fuels, the best luck we have had is with the Hydroscopic media filters, T&C was tip off back in 04 from a reliable source from Cummins that the Factory filtration for water was inadequate on 5. 9 Dodge Cummins applications,(it seems to just get the job done for Particles) . It was at DC demand that system only used 1 filter and was engine mounted. The only way to almost guarantee that the injection system will not be affected by contamination is to install Auxiliary tank with correct filtering and then pump to primary Factory tank. The correct filtering will drop 16 GPM pump to 5 GPM even the most robust aftermarket pump will not suffice for treatment to engine function, again this may sound like over kill, but it’s the only to 99% surety, Now add Bio-Diesel to this equation and a new set of problems develop, all of this can become with just the knowledge of its existence.