Randy,
My problem was at the exterior interface with the hull, the shaft lip seal and the SS face plate. It was the worst of all situations. Our fix was to patch the holes with Marine-tex, and the use of lots of 4200 on the bottom at top flanges. With respect to cleaning the Al, we just ground it down to clean Al followed with the Marine-tex. It's working with no problems. The real/intended seal area is between the bottom SS flange, the hull and lip seal adapter. The use of 4200/5200 is the std/preferred set-up performed by the Naiad rep. If you have water leaking into the area from the top, you need to add more 4200, or you may have a leak in the internal wooden or fiberglass adapter area. I would suspect that if water is getting in, it is from the bottom interface, and not the top flange, because it should have minimal exposure to water from the inside areas. The internal hole is of no real concern, assuming you have a good seal at the bottom and top flange area, and that when sealed, the area has no other sources for water ingress.