I don't have the same size boat as you, so I don't know exactly which portlights you have. That aside, I will make a general comment about rebedding them. Opinions vary. Butyl tape is one option that some people favor. Others prefer a flexible sealant that sets up, like Sikaflex. In either case, a common concern is being sure to have a thick enough margin of sealant to allow for the movement that will occur when temperatures change & dissimilar materials expand different amounts.