Sorry for the tardiness of my reply, weird work schedule.
Long ago,
@Babin Farms suggested the Peel N Seal, and it seems like it's become the defacto solution to sealing that cleanout tray. I personally haven't been able to use it, but not for trying. It may have been the weather, time of year, or just a bad tube. I think it was ultimately a bad tube, but I do know it's a good suggestion, as it's designed to be applied and removed easier than most other sealants for winter weatherization.
I was just tagging him in, and giving credit to the originator of the idea. He's kinda handy in the fixit department, and it's always good to get more eyeballs on your problem.
As
@FSH 210 Sport mentioned, Jet Boat Pilot sells a riser that puts that hatch about 3/4" higher, which seems to be enough to allow the water to drain out before getting in through the (loose-fitting) inspection hatch you circled in red.
Check this thread out, from the links in my signature as well, if you want a far cheaper option:
That’s a great video. I have removed the larger tray and resealed and still get a ton of water. Did you do the reseal and add the riser at the same time or separately? I’d hate to spend the money on the riser and keep having the same problem.
Fab one up, DIY style, for ~$20-25. Not sure if yours is the same size as mine, but I'm damn near convinced I could have used the scraps and the adhesive to make the second layer, instead of buying 2 boards, and it would have been about half that cost. Might not be worth the hassle though, since they're only $7-10 each. Mine is also 1"...
The cleanout tray is designed to mount the cleanout tubes, as well as give you more and better access to your bilge and the transom area of your boat. While you don't (or won't) have to access that area often, you definitely DON'T want to seal that off with 5200, in case something happens, like the criiminally horrible crappy plastic scupper cracks and starts to allow your boat to fill up with water and sink(ish). You also have quite a few hose clamps in there, and if those rust or break, you'll need to access those. All of this to say, there's no need to permanently seal it up, but there's DEFINITELY a need, oftentimes, for people to seal that tray up to stop water ingress, and the Seal n Peel is way easier to deal with than silicone, while being adequate enough for this task.
One thing I learned from
@zipper and others here, is that 5200 CAN be drilled/tapped for screws. I'd use it to address any issues with the screw holes for that cleanout tray. Put some tape or something on the underside of any bad hole, apply 5200 and when it's cured, drill/tap for screws, for a better hold than the fiberglass in that area.
Not sure where you're at, or if you boat in fresh or salt water (gotta add your location to your profile), but the hose clamps DO go bad. I don't know if Yamaha uses stainless, but there's enough folks who've had loose clamps from the factory, and others who have had them all rusted out. The best option for hose clamps are spring band hose clamps, but I haven't found those in stainless (or really looked, for that matter), so that's the reason for my suggestion of the T-bolt hose clamps. They offer more consistent clamping pressure, and to me, they're just easier to deal with, and can be found in stainless for less worry. Dunno what size you need, but here's an example of the clamps I'm suggesting:
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