I don't know much about Chris M's ignitions, which I hear work really well, but they make ignitions that produce only the juice you need to make spark. Which means you don't need to run a battery. I have a Boyer Racing ignition that operates this way but runs off of the charging system. I don't run this in my 250 because the charging system weighs a little over 6 pounds. 3 and a 1/2 of those pounds are on the crank. You can't just wire it different with out something to change the voltage. Your charging system puts out AC and your bike runs off of DC. If you want to try it.... You could try running a 12 volt Tympanium ($50) which does exactly that, turns AC to DC. Like the band. It only has 4 wires, the obvious ones, 2 for your alt. and 2 for your main power. It's easy enough that even Jeremy could hook one up.
Aaron