If you go with the 12 volt coil and ditch the 6v it should be pretty straight forward. I just rewired mine when I replaced the generator with an alternator, I replace every wire on the machine and added a couple of things. I wish I were a better artist I would draw it up for you (even though I am far from an expert), I figured it out.
I can try and write it out but it just might confuse you..... My alternator was one of the one wire jobs. I ran a wire directly from the alternator to one side of the ammeter. On the same side of the ammeter as the alternator wire, I ran a wire down to the positive (always hot) side of the starter switch (same spot as the positive from the battery goes). From the other side of the ammeter I ran a wire to the ignition switch. From the other side of the switch, I ran a wire to the + side of the coil so that the coil gets power when the switch is "on". I think that is it for the charging and ignition circuits. I am going by memory, I am sure some of the folks on here know it better then I do. I installed a 12 volt accessory plug, both headlights, a new switch and a couple of LED warning lights at the same time so my memory of these circuits maybe off, but I think that is correct.
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