Captain,
You've started another thread covering the same problems. I moved it to the 'Troubleshooting' section from 'The Tavern'.
You'd be better off to keep your current issue in one place >
http://motorbicycling.com/showthread.php?t=57907 so it continues to get coverage as opposed to posting in multiple areas of the forum.
How fast are you spinning the rear wheel when you're testing for spark? You might not see any ignition if the wheel is rotated slowly. It needs to spin pretty fast. Try suspending the bike so the rear wheel is off the floor and with the clutch engaged pedal the bike as fast as you can with your hand.
Make sure the spark plug wire is connected properly and that the wrench flats on the plug is in good contact with the cylinder head cooling fins.
As I told you in the other thread, the kit plug boot is notorious for bad electrical connections. It might work, and, it might not. You've already had problems with the boot and said that you've "fixed it". That makes me suspicious.
At your first opportunity replace that boot with a good one. Any auto parts store will have plug boots that have a metal snap-on connector that should provide a good electrical connection. You'll need a spark plug with the top cap installed and not the kit plug which relys on a connection to threads where the cap should be.
The push-on connectors on the blue and black wires are not the best. We typically suggest that those connections be soldered and protected with heat shrink tubing. I once had an engine that wouldn't fire and it was discovered that the connector was crimped onto the blue wire insulation and not the conductor. This probably isn't your problem because your engine did start and run, if only for a short time.
Although it is mentioned a lot, (I've only had one in many years that was defective), but the kill switch can apparently also give you problems. You might want to try the ignition test with the kill switch wires disconnected from the blue and black wire.
Tom