Well the, seemingly best, trick for our CTs, is to convert to a single, FULL wave, DC setup.
Our bikes stator/magneto's are split into 2 different circuits...sounds like yours is the same... So you get rid of the center tap from the lighting coil, then use the entire lighting coil to power 1 DC battery circuit, to power everything.
But that's usually done for 12v systems. I'm not sure if you can do it with 6v systems or not.