02 polaris Trailblazer running issues

Hi I have an 02 Polaris Trailblazer. it will crank right up no problem and I can ride all day, but the first time I hit water (small puddle) the bikes falls all over itself, it takes a min to crank and when it does it wont idle without help, It wont rev up. I can hold the throttle down and it wont move. I can work with it and get it to wind out in neutral eventually, but I put it back in gear it wont build up the rpms. I feel like its trying to start out in 5th gear. I can let the bike sit for 30 mins or so and it will crank right back up and take off no problem. I have cleaned out the carb, changed out the petcock and plug. air box is dry, plug wire looks good no slits or holes. the clutch seems to be functioning properly. I had a shop look at it but were not able to recreate the problem with a hose, neither can I. my guess is its something electrical or carb related but I cant figure it out, any help would be greatly appreciated.