top cap joint to gunnel- 1974 20 SF

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My 20 sf( i'm finishing up on someone-else's rebuild) that doesn't show much progress since the wedding in July, or no two months before that even, has the joint where the cap meets the gunnel. When the cap sat back down, it doesn't line up perfectly or sit down on the boat totally flat either. What is the best way to seal this and to make sure it is strong enough?