Wow! Nice work! Let me answer your questions one at a time:
1. Especially if you precoated the bottom-side of the plywood with epoxy prior to glassing, I recommend counting the epoxied fiberglass as the first of 3 coats of epoxy that the bottom side of the deck pieces get. NOTE that right after this 'first coat' is when you want to seal ALL plywood edges of the deck. This is only necessary for both deck pieces and the top edge of web stringers that are under the deck - you cannot built fillets that hide and seal up the unseen plywood edges, so you have to seal them very well prior to final installation and the building of fillets on the top side of the plywood. OK? I seal edges by first coating them with epoxy (a roller is great and fast for this, even though the edge is narrow) - adding more epoxy until the edges stay fairly shine. Let cure, scrape drips off the plywood faces if you have them (carbide scraper) and sand the edges - vacuum and/or wipe them off well. Mix a creamy-thick blend of silica and epoxy and use a putty knife to smear the silica mix into the edges of the plywood. Use your gloved finger to lightly rub the mix into the end grain and let it cure. Now finish those last coats of the epoxy, rolling it both onto the fiberglass and the edges. This sealing works well because a) the initial coat wicks into the wood cells and mostly seals them, then b) the silica mixture smooths and seals the end grain nicely, then c) the final coats of epoxy fill and seal - putting the finish on. Do this, and you'll never have deck rot.
2. You want to isolate the fuel components from the interior of the pilothouse and/or cuddy - the main issue being fuel fumes traveling around under-deck until they get to non-spark / spark-proof electrical devices that risk igniting the fuel fumes. It's a safety issue. In the open cockpit, this is not an issue, however. Use double clamps on all connections and try to lay out your fill/vent/fuel lines so that it's easy to isolate them from inside the pilot house and cuddy. Note that 'isolate' means under the deck too. For example, if you have a belly tank that extends forward under the pilot house decking, then make sure it's sealed on the sides and forward end (but it's OK to have a drain plug through under-deck bulkheads as long as you keep them plugged unless necessary to temporarily take them out - say for cleaning). Think through your routing of hoses and try to make it simple on yourself ... boxing-in can become overly complex sometimes.
3. A 200 hp motor is great ...
Keep the pix coming!
Brian