Here's what I did to solve that problem. Keeps the bulk of the water out, and doesn't look like a complete cob job. I made a template out of 1/4" plywood, kept trimming till I got two, symetrical pieces, then traced onto some smoked lexan and copied the screw pattern of the transom cap. Worked out good.
I know the feeling. I have a 75 proline flatback that was redone in 2003. The rebuilder added a suk df140 and a jackplate. The boats scupper are now below the water line with just one person at the transom. Hence when you take a large amount of water on it will not self bail as the scupper are underwater. Only choice is to put a bunch of weight in the bow or get up on plane. The scary part is if you are dead in the water the later option is not available.Any thoughts on how to handle fixing this issue.