I would think that you would be better to run one double ended coil firing every revolution with a wasted spark. Assuming you don't have any plans to go to 180 or 90 or 270 or other crank configuration that is.
1 coil to hide in place of two. Won't that alternator work as 12V or is the stator the wrong type? I am sure that I ran my last T100 (57 variety) with 12v from an alternator but I don't recall how many wires it had. I ran a cap and zener diode regulator and simple rectifier IIRC and mine had a K2F magneto for sparks, so that was a minimalist lighting circuit. I never had any issues with mine that way.