One issue is that you let it idle for a looonnnggg time: 30 minutes... When the engine is turning less than 2,000 RPM, the alternator will
not put out enough energy to charge the battery; the ignition system, as well as everything else, will run off the battery, draining it (starting the engine will drain the battery of a large amount of stored charge; then the headlight, alone, will draw ~4.6 Amps, plus the ignition system firing the pistons, and you have a heavy drain on the battery, which gains nothing from the Alternator at 1,000 RPM -- normal idling speed).
Visit the Home page of this site, and download the FSM (Factory Service Manual) for testing procedures for the Rectifier/Regulator, as well as the Alternator. Cheers!
1979 CB750K (sold, 2012, but not forgotten)
1983 Kawasaki 440 LTD Belt Drive (sold, 2011)
1993 Kawasaki Voyager XII