i wouldnt pull the battery lead because it isnt a real alternator... i could be wrong, but i dont think it will continue to run.

i would take votage readings with the bike off. you should have 12v on either battery with a full charge. test voltage at idle, and then at 1/2 throttle, and then at 1/2 throttle with the lights on! how much does it drop with the lights on?

i dont remember for sure, but 1/2 throttle should get you somewhere close to 14v, but not over!