I'd start looking at a couple of areas:
1. Check the vent hoses from the bottom of the carbs and the drain hose from the airbox. If they are missing or pointed forward or toward either of the wheels, water could be working it's way up into the airbox or carbs. Check the hose routing.
2. Check the air box and snorkle area. Could you be missing some of the rear fender? Maybe your throwing water from the rear wheel up into the airbox.