It sounds to me like your battery had an internal short. That's really the only explanation I can think of for the lights acting the way they did, flashing and such. How old was the battery?
Bring the old battery to a place like Interstate Battery, they can test it for you.
Quick way to check the charging system... measure the voltage on the battery with the bike on but not running. You should see somewhere near 12 volts. Start the bike, the voltage should jump to near 14.4 volts.
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