One thing about running the bike for 3 hours.. You should have an idle of 2800-3000 rpms in order to charge the battery. If it idled at the standard 1000 rpms, that might be what caused the drain (Unless of course you know that you have a bad leg on the stator)
A bike can run with two of the three legs good, it just won't charge the battery.
One of the reasons is it nice to have a voltmeter on the bike. You can tell instantly if you are charging or not.
Patriot Guard Rider
2000 VN750 Sere (Serendipity)
1990 GL1500 (Ole Blue)
1986 VN750 EVie (project bike, heavy custom)
VROC # 11628 / 25000-H
ARVROC # 12 Coordinator and Crowd Control
OKVROC # 18 (H)
TNVROC # 45 (H)