This advice is maybe too late, but you are figuring out that Seadoos use coolant for engine cooling, but river water for exhaust cooling. The water in the exhaust is normally blown out when you flush the ski with the engine running. So just make sure you get water out of the intake - the water in the exhaust will naturally blow out when you start the engine. I am a little concerned the exhaust muffler or box could have split from the freeze, but you wont really know until you start it with a hose connected and see if water leaks into the hull. Whatever you do, dont turn your hose on until the engine is running, and turn the hose off before you stop the engine. You will fill your intake with hose water if you dont do it right. Watch some you tube videos of how to flush a seadoo before you start it. When my seadoo sunk, i idled for 2 hours around the lake with the oil cap off to boil all the water out and get oil clear, and then changed the oil one last time. I had to change my fuel injectors due to water exposure, ran poor, but i had salt water in my engine. Been running great since though, and that was 3 years ago. You might also need injectors too. But your electronics all seem good, which would be my biggest concern with a salvaged ski.
Another secret for your next flooded ski - you typically don't need to take off the intake to get the water out. Just remove all the plugs, and put a wet/dry shop vacuum on each cylinder hole while you crank over the engine. Crank for 20 seconds or so sucking water out of each cylinder. Repeat process for each cylinder 2 or 3 times until all water is out. It will suck your intake dry - works great! A master jet ski tech gave me that advice when my ski sunk.
I have two 2014 Sea Doo GTX 260is limited. One of the two had milky oil (water in the oil) from a bad intercooler when I purchased. I don't know how long the water was in the oil prior to my purchase, but I cleaned it out as soon as I bought it. Multiple oil changes later, and with a new intercooler, the oil was pristine. I cranked her up and rode for about two hours. The next morning I rode again and after about 5 minutes the engine shut down and would not restart. I got a tow in and took her back home. Long story short, I lifted the valve cover off to find the timing chain broken. I have since learned the timing chain is the weak link in this engine after water ingestion. The water in the oil caused pitting and corrosion on the chain which weakened it and finally caused it to fail. The carnage was widespread: broken intake side rocker arm, 8 of 12 valves bent, bent piston rod, and a scratched up piston. My point is a broken timing chain may be in your future. If for some reason you need to go into the engine, replace the timing chain. Even if you don't need to go into the engine, replace the timing chain over the off season. The new chain will save the carnage, the headache, and the expense of rebuilding the engine. PS: One week after I rebuilt the engine, the throttle body went out. Replaced that and now she back to running good as new.
@@SwampBoysGarage I'm no pro either. I learned the why regarding the above watching Ernesto on the Calas World channel. Awesome seeing father and son work together on a project. Many good times and best of luck to both of you.
Add a bit of oil or Marvel Mystery Oil to each cylinder. It will assist in the lubrication of the ring of the cylinder. Cycle it over a the compression should come back to normal.