I got all my surfaces clean. I am planning to use a skinny drill bit in the slot in the deck to de goop it and give my sealant something to adhere to. I may even expand the slot a bit to allow sufficient sealant in the gap. I am also going to countersink the screw holes.
Follow up question:
When these were installed- or re-installed- a layer of caulk/goop/sealant was used between the stainless and the interior boat surface. (unfortunately some of that bond was stronger than the gelcoat/glass bond) Is there any reason to use sealant in there? Or on the bolsts?