Lucky, the issue with your bike stalling at the red light is eerily familiar of my issue. Before you tear into the alternator cover, in addition to the air mixture screw rebuild kit, try blowing out the air mixture screw and pilot jet holes with carb cleaner and compressed air like I suggested. Also, have you had your carburetors balanced recently?
The symptoms sound more like an air/fuel ratio issue than an electrical/ignition problem.
Three Carburetor Problems:
Rich Mixture means the carburetor is delivering too much gasoline. Typical symptoms of a rich mixture are:
Poor fuel economy
Choke not needed from cold starts
Sooty or black spark plugs
Sooty or black muffler end pipes
Strong smell of gasoline when machine is at idle
Uneven running (will often slow from regular idle rpm's and stop)
Lean Mixtures means the carburetor is delivering too much air. Typical symptoms of a lean mixture are:
Backfires as the throttle is closed (primarily during coast-downs)
White or light grey spark plugs
Requires excessive amounts of choke to run/start
White or light grey muffler end pipes
Bluing (on chrome systems) of the exhaust header down-pipes
Incorrect Adjustment applies to carburetors that have incorrect adjustment of the air/fuel screw and the balance between two or more carburetors - where fitted. Incorrect adjustment can produce any of the previously noted symptoms. On multi-cylinder machines, with separate carburetors for each cylinder, the following symptoms are typical of an adjustment problem:
Poor overall performance
Rattling sounds from the clutch
Engine tends to stall easily
Poor fuel economy
Misfires and/or backfires
Edit: I also found this to be very beneficial for understanding how each of the different components of the carb work. I was completely clueless.