Eric,
Four pin CDI systems are much different than the more common 5 and 6 pin CDI's. All CDI's run on a fairly high voltage supply (100-300 volts DC) which charges up a large capacitor, then at the proper time dumps the charge on the capacitor all at once onto the ignition coil primary. Most CDI's get their high voltage directly from its own high voltage winding wound on the stator. Your CDI gets its high voltage from a DC to DC switching power supply inside the CDI which steps up the 12 volts from the battery to the couple hundred volts required to drive the ignition coil primary.
I don't have a picture of a four wire CDI. Airmobile101 has the following picture on his personal album page showing the connections:
ATVConnection.com ATV Enthusiast Community - AIRMOBILE101's Album: Some pics - Picture
BLACK=12VDC/HOT
BLUE/YELLOW=Trigger PULSE
BLACK/YELLOW= TO COIL Primary
GREEN=GROUND
You said you were messing with the stator wires when this stopped working. The only connection from the stator to the CDI is the trigger pulse wire. Look very carefully at the trigger wire coming off the stator. It will usually go through a connector of some sort near the stator and then off to the CDI. That is the most likely failure point. If you find your wire colors are different from the ones Airmobile101 published, then identify the CDI pin that is the trigger wire, then note what color wire plugs in there. Then look from the same color near the stator.
Another approach is to unplug the CDI and measure the wiring harness pins for proper operation:
1) +12 volts: Should be +12 volts when the ignition switch is on, and zero volts when the ignition is off.
2) Trigger Pin: Should measure 0.2 to 0.5 volts AC to ground when the engine is cranking (note this is AC and not DC volts). Another test: Measure the resistance of the trigger pin in the wiring harness to ground (do this with the engine stopped). It should be about 140 ohms.
3) Ignition Coil: Measure tthe resistance of this wire to ground with the engine stopped. It should be about 2 ohms.
4) Ground: It should read zero ohms to ground.
Kill Switch: There are only a few practical ways to shut down the CDI and kill the spark. I don't know how your quad does this, but here are the ways:
A) Disconnect the 12 volt power to the CDI.
B) Disconnect the CDI ground wire.
C) Short the Ignition Trigger pulse to ground
D) Open up the trigger wire connection from the stator to the CDI. In this case the switch would have to be in series with the stator output on the way to the CDI module.
By going through the tests #1 - 4 above with the kill switch in both positions you should be able to figure out how the kill switch is wired up.