It is worth the time to also check the connector from the alternator under the seat beneath the plastic cover near the air filter opening. More than a few of us have had that connector fail (mine had gotten hot and melted one wire out of the plug-- fixed it by cutting both ends of the connector off and soldering, shrink wrapping and taping the wires up) and if you've done the charging system mod, enough current will get to the battery to run everything, but not the full available output from the alternator. The electrical gurus here can explain.
