Have you opened the gas cap when this is happening to confirm the vent hose issue as already suggested buy Micah? In heavy rain, the water from the front tire appears to end up hitting the vent hose for the fuel tank. It is situated directly behind the engine by the swing arm. There is also a vent hose for the float bowls and 2 hoses with plugs in them to drain the air box. Make sure you trim the one from the fuel tank. The tip over valve is situated in this hose and it sits just behind the carbs. I had the same problem where my engine would barely run or outright quit in heavy rain. Cracking the fuel tank would keep me going.
