rancher stalling in water

While riding my 2006 Rancher 350 and getting into a little mud and water the bike stalls out. Noticed that it does it when the water is about 4 inches up from the bottom of the motor. When the bike shuts off and I sit it the middle of the mud hole for around 20 seconds or so the bike will start back up and be a little sluggish but it normally stays running long enough to get the rest of the way out of the mud. This issue has been going on for some time now and I have tried almost everything to fix it and nothing seems to work. Even tried to spray water all around the motor while the bike is running and can't get it to shut off to help pin point the problem. I think it has to be an electrical issue but need to know where to start. Just had to put new rec/regulator on and was hoping that would fix the problem but it did not. Bike runs great when not in the mud or only in mud that is not deep at all.