I'll second Larry's comments on the cockpit scuppers -- much better above the water line verses in the engine room --(What were they thinking).
I suspect that if your thru hulls are original installation they need reseating at best and replacement if possible. I found the Black marelon (sp) very easy to work with.
Your current valves (assuming they are like mine old ones) have a rubber center that when you tighten the screws opposite the valve lever will squish the rubber and should stop any leaks.
But - if the rubber sticks to the sides of the cylinder and you force the lever open/closed the rubber can tear away and NOT open or close but the lever will LOOK open or closed. Therefore the valves need regular maintenance / exercise -- I added a grease zert and used water proof grease from time to time before they were replaced.
Location on Pygmalion
Hope this helps
Jay