What model ski and how many hours? Most common entry points for water ingestion on a running ski are a blown head or exhaust gasket (rare for a new ski). Water is normally in the water box and is far enough from the engine as to not be potential source. Other causes are sinking the ski (includes flipping it over for some models), improper flushing, or improper towing of the ski.
If the engine is running and in good mechanical condition, you can actually get a significant amount of water in the hull without any problem. The fact that your wife was riding the ski when it quit makes me think of a blown gasket. Other potential source would be that the ski quit for other reasons, then when you had it towed in you pushed water into the engine (unless the cooling water inlet is blocked off you can't tow safely above 5 mph). So the cause for the ski to quit, and the water ingestion could be separate problems.
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2008 Yamaha FX HO Cruiser
2010 Hurricane Sundeck 2100
Last edited by Ernest T; 07-30-2011 at 09:43 PM.
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