Karl,
I would consider talking with the engine manufacturers marine division. They must have a course of action to handle this problem as a routine. It is not an uncommon problem in boats. Someone can scrub the existing fuel but without some form of biocide it will likely be impossible to eliminate the source of the growth. My guess is that they will want you to get the fuel scrubbed to remove the bulk of the problem and then kill the rest with biocide with some additional fuel filter changes as part of the procedure.
Later Ed