As of right now I still don't really know what killed the CDI. It just seemed like over volting or a bad battery caused it, or maybe a short because of the bad taillight all rusted.
Dad-blame it, quit saying that!!! Why do you believe the CDI is dead? The CDI runs on AC from the exciter coil, not DC battery voltage. The CDI cannot be "overvolted", as you put it. The CDI cannot be affected by a bad battery. The CDI cannot be affected by a shorted tail light circuit. Forget about all that... your CDI might be perfectly fine! THERE IS NO BATTERY VOLTAGE EVER BEING SUPPLIED TO THE IGNITION CIRCUIT.
The stator has seperate windings? I didn't know that. And I don't think the wiring harness was messed with.
Yes, the stator contains the exciter coil windings which supply power for the ignition system only. And has entirely separate alternator windings that supply power for the battery charging system only.
I tested the two yellow wires (all according to the manual) and the resistance was supposed to be 0.1-1.0 ohms, and with my meter's dial set to 200 ohms nothing was picked up. It also said to check continuity between the yellow wires and ground, and once again nothing was picked up. Note that I checked my meter by touching various body parts on the atv with grounding, and it beeped with continuity.
Try turning off the continuity test mode on your meter and move the dial to a lower ohms range setting.
I get about .6-.7 ohms between my two yellow charging lines off of the connector, which is within range, but there is continuity between the wires! It beeps either way no matter what polarity of probe between the yellow wires, but it never did this off of the connector from the charging coil. So why now? With the the ohms in range, but continuity I don't know what this means, as the manual doesn't specify if there should be continuity.
Again, turn that confounded continuity beeper off and read the Ohms of resistance measurement only. You are measuring resistance in a circuit... not trying to detect a short or disprove continuity. Those are two entirely different functions that your meter provides.
You've gotten way off track. Now you are checking the DC battery charging system components rather than the ignition system components. Those two circuits are 100% independent of each other. The ignition is a closed AC-CDI system with no connection to any other circuit on the bike.