Mike
It is my experience that polysulfide is hard to beat for everything that is not plastic. Polysulfide will soften plastic, so it is no good for plexiglass ports, etc. But for everything else, it is great. Smells like hell, but seals great and stays flexible. If you use white, keep in mind that it will yellow with exposure to UV. You can get it in black and mahogany as well.
I am going on the assumption that all the holes that penetrate a cored area of the deck have been overdrilled and sealed with thickened epoxy. Is this the case? If not, that is a must to protect the core from water intrusion.
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