I took my rig out this weekend for some bow fishing and riding around. Ran great for most of the day, but on our way back in we hit some rough water. Ran great till we got a mile from the boat ramp then started acting up. It would make a popping noise, like it was back firing or something. The popping noise would come out of the carb. The first time it popped, it blew my air filter cover straight off. I would try to go, and it would just bogg down, almost like it would do if you were to pull the choke out while running. I took it out of gear, then gave it WOT. It started being normal again. I put it back in gear, and ran like there was no problem. I'm not sure what the culprit is, but it did this same thing last week when we were down on the coast saltwater fishing. This was the first time it had done this. Almost sounds like the choke is pulled out, but it isn't. I took the air filter off and looked down into the carb. The butterfly was working properly, and did not look like it was getting hung up or anything. It is hard to explain, but when you give it throttle it starts popping and blowing air out of the carb. I looked around for some possible issues, such as bad gas. Put new gas in it, and it did the same thing. Weird thing is, it has only happened when we hit rough water. Not sure if this has anything to do with it though. Anyone had this problem before? Any suggestions on what to take a look at? Thanks for the help guys.

you mentioned it only happened in rough water... was water spraying on da engine? if that's when it started it could possibly be a damaged plug wire. if you run it in the dark you may be able to see it arcing at the damaged spot & tape it up.

you even look at the plugs yet? That might tell you a lot.

Do what stumpgrinder said. Sounds like you have a cut in one of your plug wires.

Popping noise happened to me when I was running ended up being a chaffed wire under the tilt / trim panel it had gotten worn down and was shorting out on the motor causing it to miss... Electrical taped it and I was off & running again.

Could be several things but if it only happens when wet then its possible its electrical. Either plug wire (as stated above) or the ground wires going to the coils (for kill switch, key, oil pressure sensor).

Thanks for the help so far. I will take a better look at it this week and see if I notice anything.