I think what you are going to be fighting is mold/mildew. If possible, I would button the boat up with a dehumidfier inside of it, rigging a hose to it for drainage. If this is possible, remove the batteries as the dehumidifier will dry them out as well, thereby ruining them. They belong elsewhere on a float charger. The dehumidification will do nothing but good for your engine as well, although you may wish to fog it, and give your diesel fuel to someone who can use it. You may try treating the fuel, to greater or lesser success, with a biocide.
“Scientists are people who build the Brooklyn Bridge and then buy it.”
Wm. F. Buckley, Jr.