So for some reason when I would reduce the thrust to 0 on my remote control a seemingly random motor would at seemingly random times go into what appeared to be full thrust.

While debugging I noticed that sometimes when I would go to 0 thrust the motors were being set to 1% thrust. I added this little tidbit to avoid the dreaded 1% thrust and that seemed to do the trick. I no longer get the sporadic beahvior.
Fixed a "kill switch" bug where I was examining the target pitch and roll instead of the copter's recorded pitch and roll. This fixes that issue.