Well gosh darn, your definitely not the first operator to make that mistake. Do you have a operators manual? If not they are available on the BRP website? Essentially it tells you if it’s been submerged for more than 5 minutes and has water in the exhaust or intake manifolds it needs to go to the dealer immediately. So items in the operators manuals like checking the oil etc, BRP engineers decided that the operator is able to perform this task. When it says take it to the nearest dealer a bell should go off, because the BRP engineers now don’t believe “most” operators can handle the process. At the very least you have to be able to access a Sea-Doo Service manual and have a pretty good idea oof how things work mechanically to DIY your Sea-Doo.
If there was water in your intake and exhaust manifolds and then you started it all that water is now in your engine and by immediately or timely the operators manual is telling you that water and metal make corrosion and that’s no good for a motor.
Salt water really bad , fresh water just bad.
Now you have kind of a mess, and I will let members with more knowledge take it from here but I would say some engine work is imminent.