Looking for advice please...went to check on our boat and found that the roof had leaked and not only mildewed, but rusted our new hatch cover that we just had redone along with a brand new cover. Does anyone have any advice on any products to use that is not aggressive on vinyl?

I like the c-49 product from Malco. You can just ask for the "pink stuff" as most people call it. Most vinyl will tolerate it without having to dilute.