I was able to solve this by switching to pycharm, for some reason spyder did not want to cooperate, kept getting DLL not found errors, "application failed could not find or load qt plugin could not be initialized", and importing QCharts would not work. everything seems to be working now thorough pycharm.
So you're right, it does appear to be a logger issue rather than a Qt one. It wasn't crashing the program at any point, but rather complaining about object cleanup order. Because of the larger structure of our code files, I couldn't assign the logger to wholely be a child of the QMainWindow, but putting the following code in the quit procedure did silence the messages.
Sorry, I figured it just failed on the last item in the list above. In any case, I just downloaded the offline version of the installer and it worked fine. This gives me a short cut to Qt Designer so I don't need the kit for Python.