I agree with pufferpunk. We have tried many, many, methods over the years to try and fight the Marine demon. Eventually it became apparent to us all that the only sure-fire way of beating it was to remove the livestock, and leave the effected system "Fallow" for several months at least (longer, if your patients allow you to).
As for the removed livestock, I suggest that you treat them in a quarantine tank with a good Marine itch medication, with all carbon removed from the filters, and skimmer OFF! Furthermore, I have found that medications are more effective if left in contact with livestock longer, ie, if the instructions say 7 days exposure, leave it for 21 days.