I replaced the floor in a Glastron Tri-hull many years ago. It is a big job, but you have already completed the worst part.
Use Marine plywood, not just exterior. Marine plywood has better plys with no voids. Just a little more expensive but well worth it.
Use your original parts as templates. Once the parts are cut, coat them with fiberglass resin. Put fiberglass cloth at least on the top.
You can order stainless steel flathead self-tapping screws from Graingers that will make screwing the floor panels to the frames much easier.
I like the idea of creating a lowered compartment for your bait tank. Are you sure that will be your last tank? The SBT 2's are a lot better tanks.
If you run anything under the floor, assume you will need to replace it, so incorporate ports into your design.
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