The air conditioning ducts are good bet...
You've eliminated just about everything else...except possibly the shower sump or a bilge area that's trapped water below the cabin sole...due to blocked or never-installed limber holes in the stringers. If your icebox or fridge drains into the bilge that's the most likely source.However, if the source is the a/c ducts, you'd only have odor when the system is running. So if you leave it off while you're away from the boat, it's unlikely. However, there is a product just for use in AC vents called GelAire...you can read all about it here: http://www.gelair.com.au/index.htmlIf stagnant sea water trapped in the toilet intake were the source, the odor would be pretty much confined to the head and would go away after flushing the toilet long enough to clear all the stagnant water out of the toilet...so while it may be ONE source of your odor when the boat has been closed up, I don't think it's the only one or the main one. If you decide to convert to fresh water flush, you'll have to replace the toilet with one designed to use pressurized flush water...there's no way to connect ANY raw water toilet to the onboard fresh water system without risk of polluting the potable water supply, damage to the toilet, or both. Every toilet mfr includes strong warnings against doing it.If the water heater were the source, you'd only have odor when you run hot water...so I don't think that's your source.The best I can do from here is tell you to keep looking. Odors are always strongest at their source...so start sticking your nose into lockers and other enclosed places immediately upon coming aboard--before you open up and air out the boat. Sooner or later you'll find it.