I know you haven't put on a after market cdi so it may not be the same as our DS but our aftermarket CDI killed 3 battery's and a Rectifier on my husbands. Have you had yours since new or did you buy it used and if you bought it used are you sure they don't have a crappy aftermarket CDI. If so get rid of it and try a new rectifier. Just my .02. I do know how frustrating electrical problems can be they SUCK. Good luck.
MG