Here's a
link to post I made on the scupper repair I did in 07. Scroll down towards the bottom of it to see the pics I posted of the repair. The photobucket link no longer works but the pictures are still there near the end of the post. The leak you describe sounds like it could very well be the scuppers.
I'm not real familiar with the fishbox up front on the CC's, but I don't think there is any wood around the drain up there. I believe that fishbox was just bonded to the hull with putty before the inner liner with the fishbox hatch was dropped into the hull. Denny