Now, you need to go through all of your spare parts when you get home from this trip and (with a good working wiring harness) check each and every part. If they work, put them on the shelf. If they don't throw them away! I suspect that without the "kill" wire inadvertantly hooked to ground, all of your "unknown" parts will work fine.
BTW guys, the real break through came not from swapping parts but when I said "ok, I understand that you unhooked the keyswitch and handle bar switch. Now unhook the black/white wire from the CDI box and see if it sparks and it did. A quick trace of all of the black/white wires revealed a connection behind the headlight that wasn't supposed to be there.