I ended up having to do the factory reset anyways. After restoring the 5 files, the phone wouldn't come out of Airplane mode, and the phone would not work. Wifi actually seemed to be working fine, despite it not coming out of Airplane mode.
If I tried to actually make a call, it just say at a screen saying it was enabling radio.
Booting up from the factory reset now, just will need to reinstall everything. It worked as far as allowing non-market apps, was able to install the Amazon app store and then install apps from it. But obviously the other issues prevent me from leaving it that way.