Don't know about the lights... if the headlights are working ok then there must be a broken connection. That's a case of continuity testing.
The misfire - what bike is it? The 996 breed suffers from poor fueling in the lower rev range, resulting in spluttering when opening the throttle, and again at around the 9k mark. This is a problem with the eprom map, and since it's mixture sensitive I'd imagine it's severity is easily weather dependant.
To tune this out the only real cure i've heard of is a single injector setup with an UltiMap chip.