had my machine do it last week,when I hit a deep water hole after being on a fast trail for a while. My reverse light didn't come on but it sputtered like the reverse limiter was reached. I have the reverse limiter bypassed with a selector switch I put in, so there was two theories, One was yes a connector was getting wet, but I have di-electric grease on all the connectors I changed. The thing could be the 3 way switch getting water into it, since it is just a plain ol' dash switch. The other thought was thast aftr riding for a bit, then boucing into a deep water hole A HUGE plume of steam came up off the engine and could have been sucked into the intake, at the same time a surge of water could have gone into the exhaust.. this could have caused a not so good atmosphere for burn, and a huge amount of back pressure. Mine came out of it as I went a little and came right out of it when I got out of the hole.. haven't been out since, to see if that was the issue or if it was the curcuit so I don't know if it was just something as simpleas steam into the intake..
Good luck and post your results if you adjust anything..