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Scrape any loose paint and clean any oil/reside. Use a spray or brush on paint for aluminum. Nothing special.

As for re-attaching cover, check the holes and if oversized, fill with marine tex and re-tap.

3M's 4200 is an adhesive sealant and is not a suggested product. I would use a standard marine sealant (NOT SILICONE). There are some owners who demand a color match to the floor. Many vinyl siding companies offer sealants in the appropriate color.

I personally used white Boat Life brand. There is also 3M 101, Sikaflex etc.

It is recommended to pull the inspection covers to allow any moisture to vent when the boat is not in use.