I went downstairs and the battery had bounced back up to 12.3V from the 5.1V it was putting out when I got home from my work commute and just started it up to see what it would do. The battery voltage immediately began to drop, one hundredth at a time, but if I revved it It would rise about half a volt, but as soon as it dropped back down to idle speed it would continue it's decline.
I started checking out the wiring in various parts of my harness to inspect connections and went down and removed the sprocket cover to check the wires as they exit the shifter cover.
I wiggled them back and forth lightly and one of my yellow wires just popped apart at what I assumed was a soldered and shrink wrapped joint! 
I won't have a chance to reattach this wire tonight, but could this be a potential source of my lack of charge?
