Are you really getting water in the carbs ? It is possible for heavy rain the block the fuel vent line, if that happens the bike will run for crap (like a carb problem) and by the time you tear into the carbs the problem will literally evaporate.
Just asking, because water in small amounts (rain/mist) will actually run better.

05 speedmaster - 1100cc, 11:1 racing pistons, Carillo rods, thunderbike cams, ported and polished head, 2mm over intake and exhaust valves, Barnett kevlar clutch, scepter pipes, oversize manifolds, 45mm HSR's, TTP stage 4 firestarter