951 cooling system...
The 951 cooling system is a bit more intricate than the others. They have a magneto and lower crankcase cooling system.
If you are not seeing any water flushing from the jet pump or exhaust during your back flush, then you do have a problem of some sort.
Do you know if you have any water at the top of the motor, where your cooling system indicator (tell tale) hose is.
What I believe your going to have to do is remove the outlet lines, one at a time and blow through them to find out what is stopped up.
Have you ever had the over heat alarm sound while the ski is running? Your main cooling water outlet from the engine drains back into the pump. You can see these lines back looking in from the inside, toward the back of the hull where your pump connects to the transom.
You have two lines, about 1/2" in diameter (actually metric). One is to supply the motor, one is the outlet from the motor. Check to make sure they are clear first. Then, you'll see two smaller lines, one drains the engine cylinders when you pull the ski out of the water and the other is the outlet of your crankcase heat exchanger. The heat exchanger would be the first thing I'd consider suspect.
Where your water inlet comes in from the pump to the top of the head, two lines break off and drop down to your tuned pipe water jacket. If your overheating your exhaust system, these two lines would also be suspect, take them off to make sure you have a flow of water through them.
You have one line that is called your "anti roll over bypass" line. This should not affect your engines cooling circuit.
When you connect to your backflush line, you can have your clamps or hoses prepared for removal. Turn your water on slightly when your hoses are ready. Do not use a full blast amount of water. When you get the water on, pull the lines going to your exhaust first. Check them for water flow.
You can only do this for a minute or so, then you'll need to shut the water off and start the motor. You only need to run the motor long enough to expel the water you have built up in the exhaust system. This goes against procedure of starting the motor, then the water and vice versa when shutting down. But, you have a cooling problem and that's your best way to check your flows. Be certain you do not run water more than a minute or so and not wide open. It should take about 3 or 4 minutes of solid water before you fill up your exhaust system to the point it overflows into your cylinders.
You also mentioned towing the craft back, and full of water. What was full of water, the engine? If so, did you tow the ski faster than idle? Did you pinch your water inlet line from the pump. You are not suppose to tow the ski over 15 mph and you are suppose to pinch your water line if you tow. On a dead engine, you have no exhaust pressure to keep water from building up inside the water injection of the tuned pipe, then, it will flow over into your engine.
When towing the ski, the cooling system will basically still be working. The pressure from your cooling system comes from the venturi of your pump. Towing, water is running through the venturi, effectively pushing water into your cooling system and engine. So, make sure you pinch your inlet hose while towing...........