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Hi and thank you for your question.
To be able to custom tailor an answer for you, and lead you in the right direction from the start, I need to know the exact make model and year of the water craft you are working on. Also, any additional information you might have about how the engine got water in it is beneficial too. One last thing is the water salt water or fresh water in the engine and how long has it had water in it? Did you dump oil down the spark plug holes after you got water out?
Thank you for the additional information. If you can get enough of your buddies together, you should be able to flip the ski upside down with the plugs out and get all the water out of the engine. Once you do that, you need to get oil in the engine to mitigate the damages.
As far as spark, the first thing you need to do is disconnect the plastic connector coming out of the handle pole that has one white and one black wire in it. With that disconnected, re=test for spark.IF that doesn't work, you are going need a digital volt/ohm meter. Do you have access to one and know how to use it?
Super. Since the entire electrical system is supposed to be water tight, I wouldn't immediately expect a problem internally with the electrics just because it filled up with water.
Best of luck, let me know if you need more help.