With the right tools, opening up a 50v's magneto is a cinch. The bolt is reverse threaded however, so be careful if attempt to remove it. On most bikes you can use a 3/8" socket wrench with no socket on the bolt, and a use a piston stop on a strap wrench to keep the engine from turning. Water is bad for electrics, but it should be alright when it dries out.
i saw this same thing happed to a malaguti once, and i think the water ruined the condensor. Its something you can test, howver, and pretty easily. Motobecane have i think three coils, and underneath the left hand one is a thing about a square inch in size and probably green. This is the condensor. if you take it off and test its resistance, and it reads about 200 ohms, then you're alright. A bad condensor will allow you're bike to spark, but won't run more than 5 minutes or so.