Baja Designs Dual Sport kit issues?

I'm having some issues with my bd ds kit (bought with the 2000 650r) originally none of the lights were working but I got that sorted out, unfortunately now the lights are directly effected by my rpm's. if I'm idling the lights flicker at a dim level, but when I rev it's almost as if I'm going to bust a bulb it's so bright. I don't really know how to charge the battery (the 10 double a battery pack) because I don't have a charger that will work, and I'm guessing my bike isn't properly charging the battery when it's running. Do you guys think it's the rectifier? How can I test it to be 100% sure? Also, how does the baja designs rewound stator work? the way I have the bike set up now is 2 wires coming out of the stator that both tested with a multimeter as putting out good power goes to the rectifier, then two wires from the rectifier go to the battery (1 for power and 1 for grounds). I'm not sure how it works as I am electronically challenged (good description for this subforum!). How does everyone else have their's run so I can learn?

Simple answers for a not-so-simple job due to the electrically challenged you
1) disconnect the light and go ride >> this should charge the batteries.
2) then connect the lights (via an Off/On switch) to the + of the batteries (assuming you have a full-DC system).
If the latter assumption is wrong (eg AC and DC system, not uncommon) then I dunno how to help you via this medium. But BD should, go phone them?