on my old boat i had a similar issue.
what i found was a few problems-a leaking hatch seal,leaky windows and the toe rail seal.
in these boats sometimes you cant see the water comming in thru these areas because it runs in between the deck and the inner fibreglass headliner.
with the toe rail however you sould see the eges of your cushions and storage shelves getting wet.
with the windows i found water didnt so much leak from where the butle seal is between the frames an the fibreglass but between the actual winow seal between the lexan and the metal frame.
these are special seals and must be replaced with the proper part, not silicone.it wont work, at least not for long.
you can buy everything you need to rectify both these issues at Holland Marine Products
and for your boat your likely looking at around $100 for everything you need.i believe they are the only place out there where you can still get the window seals.
as for the toe rail c&c used a thicker butle tape to seal this joint.
i would also check around where your rigging bolts down to your deck because as i said before the water will run thru your inner healiner and make it seem like its comming from a different location.