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