>>Has anyone every done a heart transplant like this? We've got the engine running properly, we just have to figure out how to get all the wiring hooked up.<<
As for yer four wires, You have spark-wire (the cap), Obviously one's a ground wire (unless it's a body-frame ground), One has to be a hot lead, and the remaining wire probably has to do with the brake light and/or high beam headlight...usually brake light.
As fer figuring out which is which, if you don't have the proper tools you can play mix and match with a handful of dual-filament 6V/12V bulbs if you really have to, but it's much better and easier to use a voltmeter if you have one.
Most of my "conversions" have wound up going to a simpler system than original, and using a frame-ground, save in cases where a voltage regulator or battery was absolutely required, such as a Tomos A3 or engines that use a battery so as not to blow out the headlight.
Hope alla that makes some useful kind of sense to ya,