I had this same problem when I bought my boat. I solved it by rebedding all of my deck fittings. Yes. All of them. I stopped all of the leaks, repaired a good bit of rot and put on new backing plates. It was the best thing I have done for my boat, but, not one that I would wish upon anyone.
I still got water down my mast and had the rot in the bilge problem. The following season I installed an automatic bilge pump. Bilge rot solved.
This year I am tackling the mast leak. The blocks on my mast are only about 1.5" above the top of the deck leavingno room for a proper boot. Any ideas?