Your first paragraph is basically impossible. The only way water can get inside the cylinders is thru a leaking oring, a bad exhaust manifold gasket, a crack in the cylinder or the exhaust completely fills up from the water box forward back into the cylinders. Even if one cylinder isn't firing, the engine is still compressing air.....and exhausting it. Other than that, if I'm totally missing something please let me know.
If your losing spark, why not just buy a TTO tach and wire it to read the pto cylinder? I know your frustrated, but throwing money at ideas until something sticks is not the correct way.