I'm trying to track down a leak also. I am seeing the bilge pump a few times here and there and also get a couple gallons when I pull the plug. I noticed yesterday before I pulled the plug I let the boat sit for a while with the bow up pretty high. Water was dripping out the drain plug. I just got a new plug and I can see its not sealing good. I put it in snug. I don't want to over tighten it. It just seems like a wimpy jet ski design. It is definitely letting water in. Is there any kind of upgrade for a different drain plug. This was a new plug with a new o-ring.
Lube your O-ring on your drain plug, and MAKE SURE you aren't cross-threading the plug when you put it in. That o-ring, like most plumbing fittings, does not need to be wrenched in any tighter than finger-tight+. If it does leak, it will be because the o-ring is damaged, or the fitting is damaged, in that order of likelihood. If you need to replace the o-ring, swap it out with one of the interior drain plugs for a temporary fix to allow you to use the boat until you can source a replacement.
It is VERY easy to cross-thread that plug. It sounds like that might be happening to you.
That’s the absolute first thing to verify. If that's good, then your next plan of action is to start at the front of the boat and work your way back to the stern for areas that may be causing you problems.
Verify that all the fittings on the OUTSIDE of the boat are not cracked/loose, and are in good condition. Check the rub rail all around the boat for damage or missing chunks. If not, move to the inside of the boat for the next possible culprits.
First area, check your anchor locker. Search the forums for anchor locker leak threads to compare against your boat and how it looks.
Second area, remove your cup holders, front to back, to see if they are connected to any tubing. Some DO NOT need it if they drain to the bilge, unless YOU don't want them draining to the bilge. Some will drain into your storage compartments. Fix those to have them drain to where you want them to drain. Cup holders shouldn't be your biggest problem, but they contribute to your problems.
This cleanout tray would be the third area to check, IMO. Using a hose or a large pitcher of water, open the cleanout tray hatch so you can see underneath your cleanout tray, then pour water over the area, and look to see if your tray is allowing water to leak under the tray into the bilge. If so, address it if you so desire.
You should go over these areas often, ideally before/after every outing, but at least address things from least problematic to greatest, to help you as you're trying to determine the severity of your issues. If you have a glaring issue, obviously tackle that first.
Last item is to check your interior drain fittings and plugs. If they leak around the fitting and allow water into the bilge, they might just need to be resealed, or possibly replaced. Mine had NO sealant on the ski locker fitting, and they damaged the fitting with the mounting screws, so it's getting a replacement, and I now have a replacement plug and o-ring if the need arises.