Re: Water Getting in Top Cylinder Yamaha 40hp Twin

[Don]

Not a Yamaha expert by any means…
But, you mentioned this engine had thrown a rod, so there is the possibility of cooling system damage caused when the rod went thrashing about inside the block…
BUT, I am not convinced you have a water leak. I am assuming that the combustion chamber on the left of your picture is the top/problem cylinder, correct? Yes, that cylinder is misfiring/not firing for some reason, but I am not convinced water intrusion is the problem. Do you see actual water droplets on the piston cylinder/head, or is it possible that the cylinder is just being washed clean by excess fuel?
In any event, you can drive yourself crazy trying to look for a minute leak/porous/cracked block head/exhaust cover, etc. This stuff can be near impossible to see with the naked eye.
Let’s try a different method. Get the motor started and running on a conventional flushette. Now, remove the gearcase and start the engine with no water going through it. No worries about damaging the impeller, and you can run the engine for a few minutes at idle without overheating it to see if it is going to idle any better.
If the engine does not run any better with gearcase off, no water going through it, then I think you are on the wrong track with the water intrusion theory.
If the engine seems to run better, then we can look into the water intrusion theory more. But please beware, the engine will definitely run differently with the gearcase off with no back pressure and drag from turning gearcase components. So, it might be easy to think the engine is running better when it is simply running at higher RPM with no back pressure and gearcase drag. You could always connect a hose to your water tube and run it that way to compare the way it runs with and without water.
If this test confirms your water intrusion theory, then I would connect the hose to your water tube and run water through your engine while it is not running. Remove the plugs while the water is flowing through and get a good inspection light to probe the top cylinder in the hopes on pinpointing the actual leak.
Again, have little to no Yamaha experience, hopefully someone who does will chime in….