The problem isn't so much about the water in the exhaust, but the water that got in the engine. I would get it fired up as quickly as possible so as not to lead to rust and corrosion and possible engine seizure. Remove the spark plugs and leave the caps on the grounding post. Turn the engine over to remove the water from the cylinders. Spray a little wd-40 in the cylinders to help displace the water. Hit the starter for a few seconds at a time letting it cool down abit while trying to get the water out. When it seems like all the water is out insert the spark plugs and get it started. Use the choke or a little fuel and injector oil as a premix to help fire it up. Don't use starting fluid. If it doesn't fire up repeat the procedure. Pull the spark plugs, hit the starter, insert spark plugs get it to fire up. Time is of the essence. the longer it takes to get it fired up the more chance of damage to the internal engine components. If you wait till tuesday it might be too late!
You can hook up the hose to the 2 stroke Rotax engine, and have it run for up to 5 minutes to flush it out. Connect the hose and start the seadoo. Turn on the water after it is started. Turn off the water, than shut down the seadoo. Always do it in this order.
Attach the garden hose, Leave the lid open with the blower running, so you can vent the compartment and allow the garden hose to fit properly. This also allows you to see the engine while it is running to check for cooling leaks. Start up the boat, turn on the water, in this order. Be sure water is coming out the “Tell Tale”.
You can run it for about 5 minutes at IDLE which should be at about 3000 rpm’s. When you’re done, turn off the Water FIRST, then pull of the Lanyard to kill the engine. This way it won't allow water to back flow into the engine through the exhaust due to no back pressure from the engine not running. The bearings and seals on the impeller jet pump are cooled from being in the water. When it is on the trailer it doesn't have that cooling effect so they will get hot after about 5 minutes.
I pre start my seadoo's, dry before I leave for the launch, but just for a second or 2 to be sure it will start at the launch. Peace of mind is worth a lot.
Karl