Don't forget that there are 2 vent lines to consider. One for the tank and one that vents the float bowls. Both will cause problems.
I know that the tank vent will cause the engine to sputter and possibly quit if it is in direct line with any water being sprayed from the front tire. If this happens, crack the gas cap to see if things come back to life.
The float bowl vent is probably the one causing the water problems. It needs to be located in an area that doesn't see high or low pressure otherwise you could push water into the bowls giving you your problem, or create a vacuum in the bowls giving you drive ability problems at speed (ask me how I know). I've often toyed with the thought of placing a foam filter over these vent lines to see if it would help prevent these problems.
