I don't understand the cardboard thing. I would think a bead of caulking around the outside and inside seam would seal it. Could treat the pocket in the keel with epoxy. I don't see any need to treat the keel bolts, although they could be sealed too.
What yard are you in? I might be able to meet you there and help come up with some ideas. I am planning on buying a Jeanneau so I am interested in their issues.