I tried a few other things. Tried updating in safe mode from internet, didn't work. Tried the 900mb file on usb and that didn't work. Tried unplugging and restarting, didn't work. Tried rebuilding database, didn't work. I called PlayStation and they rewalked me through everything I already did. Last option was initializing the PS4, that worked. Of course almost all of my data is gone. Save files that were automatically uploaded/saved on the Playstation Network were selective. Most of my progress is gone.
Thanks Sony for making a mandatory update which improves the quality of the system performance!