...One thing i thought was weird, i used a volt meter and one wire on the kill switch had 12 volts.
That's perfect if the switch is off, ground side switches are going away... Power is provided to the kill switch at all times when the ignition key is switched on. The kill switch, when in the "ON" position will connect it's terminals and provide that twelve volts to the CDI, which will enable the coil control.
Key on, Engine off, Kill switch off, you should see B+ on one wire, and B- (or a close approximation thereof) on the other. That is valid for a volt meter only. Depending on the CDI, some test lights can override that "turned off switch" and enable the CDI all by themselves.
Key on, Engine off, Kill switch on, you should see twelve volts on both wires, one side going in and one side going out of the kill switch.
Assuming that pans out... If messing with the kill switch gets you spark (several, not just one single spark), then don't spend a whole lot of time on most of the system. Investigate the CDI, the kill switch, and the wires in between those two items very carefully. The remainder of the system (other sub systems within the CDI, the stator, flywheel, the coil, all their wiring... You may or may not find some interrelation with the key switch there, but if the kill switch is recieving power, it's a straight shot from there to the CDI, and without the proper "enable" signal, it's not gonna run.
And yeah, CDI modules don't all interchange, gotta be real careful with swaptronics for that reason. They kinda look the same on the outside, the plugs are the same size, but on something like that it's the part you can't see where all the magic happens.