Dan,
Even though the oil was barely visible at the tip of the dipstick, you still had a bit of oil circulating in the engine, not much but some. Hopefully you haven't operated the bike with the oil light on for any extended amount of time, but my guess is, if you did you would be experiencing other obvious problems.
Might be good just to keep an eye on the dipstick level for a few hundred miles and monitor any visible leakage around the engine. Keep track of how much oil you add and the miles when you add it. Try to add the oil amounts to the same area on the dipstick. I see you're in San Diego. Maybe you can drop by the house this weekend and we can do a general overview of the bike and have a look at things. Send me an email, maybe we can set something up.
-Mike V. / San Diego
mvtv@cox.net