650/X-2 Spark problems

So I am having some problem with the x2. I took it out on Sunday for the first time. I started it up down at storage and started up perfect. Then I got to the lake and put it in the water. I walked it over to the beach and got suited up and jumped on to it and went to start it and it wouldn't start then did some test and I was getting a little to no spark ( there was water in the hull and I don't know if something got wet?) Any ways I got it back on its stand down at storage then it started right up. SO I have been starting it every other day this week down in storage on its stand and it has been starting right up. then today I got it in the back of my truck because I am going jet skiing tomorrow and I just tryed to start it and it was doing the same thing it was on the lake. Just doesn't have any spark. The hull still has some water in it so I have concluded when it is in my truck the water shorting something out so when I start it doesn't have spark until it drys out. Have you ever had this problem? Does it make any sense?
 
I don't think it would be electrical if there is simply water in the engine compartment. All the electrics are up high under the steering column. If it cranks over then it isn't your starter relay, and its weird that it starts fine while not on the water. I would either check or replace the spark plug boots especially if they are the stock ones. They don't click on too nice to the plug and can fall off mid ride. Get some nice NGK waterproof ones. Other than that always check compression when you can't get it going, could have a blown gasket and maybe doesn't matter when its on land but when it starts moving water through it messes the mixture up and won't fire. Also, try starting the ski on the lake with the hood open. Sometimes the exhaust comes apart a bit and causes problems, but it should still start up but it'll just bog out hard within a minute or two.
 
So I took it to the lake today. It would not start in the back of my truck then I went home and put it on its stand and it fired right up. WEIRD! so I got brand new spark plugs and there are after market plug boots dont know how old they are but they look good. have some extra new after market ones, I might try putting those on tomorrow night. I am going to the lake tomorrow again so I guess we will see what it does. but when it runs it runs very strong and it will run for awhile until I shut it off.
 
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