I think that the problem with your fuel right now is more than a fuel polishing system can handle well.
You need to clean your tank completely before putting clean fuel in it and running it through a fuel polishing system. I've described our cleaning efforts several times on Cruiser Log, most recently HERE
Diesel has a definite shelf life, and when it sits in a humid environment for a year or more, it degrades, algae starts growing, and you get a disgusting mixture of water and dead and decaying vegetable matter. You can use up a lot of filters removing it all, and filters are not cheap. Better to remove the fuel, siphon off what is salvageable, clean the tank well to remove all the living algae and bacteria, and then consider a fuel polishing system. If your tank isn't clean first, you will just use a lot of filters cleaning bad diesel.
For those landlubbers who say that in the army they never, in 20 years, ever had a problem with dirty fuel, all I can say is that the fuel probably never stayed in the fuel tank for more than a few days before being used and clean fresh fuel replaced it. Our biggest problem was that we believed in sailing, and just didn't turn over the diesel in our tank enough to keep nasties from growing in it.