It appears that the only area this boat could have leaked was around the  
hatch. It sounds like a poor installation. There was an extensive article in  
SAIL magazine describing the process for repairing rotten decking that I  
described. I will try to locate the article if someone is interested.
There are many products that can be used for bedding hardware. In my  
opinion, the best caulking available today is a one part polyurethane sealant.  
Sherwin Williams has one with their name on it, another is a product called NP1  
which is available at roofing supply stores. These products stick to everything  
and remain pliable for ten or more years.
 
Rummy