bighe, how much of the deck is bad? i replaced the piece in my 83 cuddy from the cabin bulkhead back to the fuel tank, gunnel to gunnel. i never took the cap off, i just cut the area out and left 2 inches where the deck meets the side and replaced the rotten part.
if you will look at the pics of vics redo of the rear deck & stringers . he never removed the cap
http://www.wellcraftv20.com/gallery/v20_vic?page=1