James,
If you are talking about the salon roof to stern (rear) pilothouse wall joint, I am in the process right now of fibreglassing mine over to eliminate future maintenance replacement. However, for caulk: remove and thoroughly clean up as much of the old caulk as you can. Apply Sika Flex 295UV. You can use Sika Flex 291 but it is not as UV resistant and therefore may need replacing sooner. For rebedding antennas, top deck rails etc. use Sika Flex 291 as it does not get near the UV exposure (or you could use butyl tape for rebedding instead).