You definitely have water in the intake manifold, cylinders, and crankcase. The good news is that it is fresh water at least - I had salt water in mine, but I won’t go into that (you can read my posts from one year ago that actually ended well - I didn’t follow everything in the manual from page 10, but it was similar and effective). But you also have another problem with no spark or fuel pump.
I suggest you reference the shop manual, but a shortcut that a very experienced jetski mechanic taught me is to use a wet/dry shop vac. Pull all your spark plugs out, and hold the shop vac hose tight over each spark plug hole as someone cranks the engine over for 15 seconds on each hole. Probably good to let the starter rest a bit, then do it again for all 3 cylinders. Do this at least 2 or 3 times for each cylinder until you are comfortable you are not seeing additional water Being sucked out of each cylinder. You don’t have fuel, but pull your throttle lever on the handle bar wide open to make sure you are not cycling the fuel injectors when cranking over the engine. This will get the water out of your intake and cylinders pretty well, without the added effort of pulling off the intake like the manual suggests. It worked great for me, and is quick and easy. With that complete, I would do your first oil and filter change... you will need to do another oil change later when you get it running and boil out any residual water with the oil cap off.
With the water out of your intake and cylinders, and fresh oil in the crankcase, you can diagnose your no fuel and spark issue at home or at a repair shop. There are hopefully others that are more experienced to suggest how to diagnose your no spark and no fuel pump - and review the shop manual for that too.
Once you are running, you can go back to the boil out procedure. I idled my ski for about 2 hours on the river with a roll of paper towels to use, partially covering the oil filler opening, with my seat unlatched and pushed way back so the engine was exposed. It was uncomfortable, but it worked. I saw my oil filler tube go a milky beige color after about 45 minutes, steam stopped after about an hour, and then the milky appearance in the filler tube went away after about 90 minutes. I idled about another 15-30 minutes for good measure. Then I did another oil and filter change, discovered rough running off idle because my injectors were damaged from the salt water sitting in my cylinders too long. After replacing my injectors, I I was back to good as new, and have been for a year now.
That is what I would do if I were you in your situation.
