What would be the downsides of hooking the 2 wires up backwards? Not the main wire obviously, but the two smaller wires that are normally in the plug. My plug disintegrated about 7 hours from home and I couldnt remember for sure which wire went where, so I hooked em up best i could remember and it charged and ran fine. So my question is, would it still charge if the wires were backwards?

Those 2 wires are the sense line and charge light. Not sure if the charge light circuit connects to the computer or hooks straight to the charge light bulb in the dashboard . If the 2 are backwards, then there would be voltage all the time at the charge light circuit and this is basically connected to the battery, so the regulator would be on all the time, if the rpms are past a certain rpm. If the sense line is connected to the charge light circuit, then the charge light would probably be out when the ignition is on. it might actually work, but if the charge light is off when the ignition switch is in the ON position, than chances are the 2 wires are backwards. The main purpose for the charge light circuit is to energize the regulator, and it also is a good indicator if it's working. Typically the semse wire is bigger. Most likely if the charge light is lit when the ignition is in the "ON" position, it should be ok.