The title says it all. Even if the intake ports are pointed down, it seems like rain would get sucked into the carb while riding in the rain. Is it likely, or am I being overprotective of my new baby?
I ride in the rain a lot with an open element air filter, doesn't seem to affect it much if any. That said, the main thing is to keep any water out of the magneto, if it gets wet it will short out and quickly die. Make the wires loop down to prevent water wicking, then use RTV silicone to seal up where the wires go into the case.