Chasing down an annoying leak can be a challenge. But it is a necessary process. The scupper valve is connecting the cockpit self bailing drain to the scupper via the white hose running through the engine compartment. You have already heard many say that changing the scupper might be important, and it is if it is suspect. The other holes in the boat can accumulate water in the boat. I had an '08 SX 230 that drove me crazy one summer. I found that the speedo cable hole that was up in the top of the recess that the jet pump was in on the back of the boat, leaked, but how could that be an issue, it is always about 8" out of the water. Well, if two of us were on the back deck at the same time, the boat would sit that deep or deep enough to let water in through that hole. If you inspect all of those thru hull holes, you will find big globs of silicone that were used to seal them. I removed most of these globs and resealed them. That solved that problem.
The clean out tray leaking is not a concern really. It has a drain line hooked to it, but that doesn't do much either. So the caulking along the edge isn't a real issue, as a matter of fact, I removed mine and cleaned it up last time I was in it. I replaced the caulking with a rubber gasket so I could get in and out of the clean out tray as necessary without all the effort. Now I just remove the screws and pull it up, fixing or installing whatever I need to, and replace the tray after. No more caulk there. Sealing the clean out tubes to the tray is not a perfect seal either, and they can leak, but you can't stop that 100% either, and I don't really try to caulk them either, just make sure the tray hole lip is inside the tubes, and the hose clamp is installed. If you over tighten the clamp, it will deform the hole lip in the tray and make getting the clean out plugs in and out harder. Cleanout plugs can leak while stationary. Under pressure, the should not leak. The design of the gasket/seal on them, is such that prevents it or should. The gasket is not 100% however in terms of letting water into the plug itself and then into the tube, so finding water on top of them, whether from slosh over the deck or plug bypass is common, and not worth chasing down if your performance is ok.
A logical approach at narrowing down the leaks will result in a dry bilge...and I think your on the right track!