" Sal,
As for the batter
" Sal,
As for the batteries - there's a million ways to do a dual battery system, but there are only three ways I can think of that the batteries could hurt anything electrical. The first is wiring them backwards; the second is putting two 12 volt batteries in a series (24 volts - ouch!); lastly, if you disconnect the batteries while the engine is running, it can destroy charging components.
As for you engine - it sounds like you have SERIOUS issues with water getting into your fuel system. The first thing I'm wondering is where the rust and all the water is coming from.. if it's just that the water separator is rusting - replace it; if you have a steel fuel tank of some sort, it's time to get rid of that and replace it with plastic, stainless, or an aluminum tank(s). If there is anything else made of steel in your fuel system up to the engine, replace that too. What I'm saying might be a little harsh, but there just isn't any tolerable amount of rust in the fuel system of a boat.
Sometimes a bit of water can enter the fuel system by condensation. If you are not keeping the tank(s) full and/or have a metal tank, sunlight can heat things up and form droplets of water. It's also possible to have water getting in from a vent or breach somewhere in the top of the tank.
Bogging can be electrical, but with water in the fuel, there's very little reason to suspect an electrical problem at this point. Bogging is usually caused by a lack of fuel (or lack of fuel that burns) getting to the engine; if the jets in your carb get clogged, with even a tiny spec of garbage, water, or varnish left over from evaporating fuel, as you advance the throttle and open the butterflies the air flow will be there, but not the fuel. A lack of fuel causes a lean mix, which creates the bog. Water in the fuel, in general, will also cause a bog as it doesn't move through the carb like fuel and won't burn.
The only real solution for you is going to be to take all fuel system components out, carefully inspect, and then flush/drain them completely - replace anything that is questionable or cheap enough. If it's about time to replace the fuel lines & primer bulb (say it's around 5+ years old), do that now. I'd think about replacing all the fuel lines in the engine too, but no matter what, they need to be cleaned after what has happened. All fuel filters should be swapped out w/ new ones too etc.. etc.. Lastly, the carbs are going to need to be completely disassembled, carefully cleaned, and rebuilt.
As for how often to change the water seperators; I've got a couple hundred hours on a rayco, and I'll replace it becuase the outside is corroding, but it wouldn't need it otherwise. My belly tank is about 40 gallons and it's plastic, I fill it after ever trip and haven't ever found evidence of water in the fuel.
Oh.. and the dry gas - NEVER use dry gas in an outboard. There are a few problems with it, the first is it's a solvent and will dislodge chunks of fuel varnish, sending them up the line toward the carb (can end up clogging a carb); the second problem is that it will weaken or even dissolve certain rubbers; lastly, dry gas is alchohol, which is a solvent for oil/fuel - 2-strokes are lubricated by fuel/oil. A marine fuel stabilizer is a good idea though, I add Penzoil marine fuel conditioner/stabilizer every fill up.
Be sure and at least fog those cylinders if that engine is sitting, as it's got some moisture in it now. Tell us how it goes,
Jon "