Re: Leaks when it rains.
Search here and elsewhere, there are plenty of threads about leaks. If the ports are leaking, there's no way to "fill" around them, they need to be removed then rebedded or replaced. Unless you are lucky and just have old gaskets that can be replaced.
As to the mast or deck...leaks can be hard to find. IMO the best method is to seal up the boat, close up all vents and hatches, and stick a heavy cardboard in one of them. Insert a leafblower or shop-vac exhaust in the cardboard and pressurize the boat, then throw soapy water on the deck. The boat will blow bubbles from where the leaks really are, and those places or that hardware needs to be removed and rebedded properly.
One big warning on the soapy water, the deck will be very slick afterwards, wash it down well before trying to walk on the soapy places. Use a brush to scrub them, and you get a clean boat as a free bonus. :-)