Make sure the battery connections are secure/clean.
I wounld have the battery condition rechecked..
Next:
Check the battery voltage when the bike is running, should be ~14v @4000+rpm.
If the volts dont come up to this value, disconnect the alternator from the R/R, start engine and check the AC volts between all 3 wires @ 4000rpm (1-2, 2-3, 1-3), ya need ~60+v on all 3 sets. if ya dont get these readings the stator is shot.. if these readings are good, the R/R is shot..
DO NOT/NEVER disconnect the battery when the bike is running.
luck