I've been through and disabled everything individually. Apparently NVidia audio and 3D surround devices were not loaded properly, as well as my LAN driver (despite both of them working). Funnily enough, when I enabled boot logging, the computer shuts down correctly! But after the first shut down it doesnt work correctly again. I tried using driversweeper, and the shut down immediately after that works too, but even if I don't reinstall the NVidia drivers, the PC doesn't shut down correctly after the first successful one either. Obviously it shuts down perfectly from Safe Mode every time, so it is driver related, I just don't know why the Boot Logging seems to allow it to shut down correctly. I've wiped and cleaned all NVidia drivers, and the first shutdown is always successful, but never after that.
EDIT: Success! It turned out to be the "MSI Super Fast Boot" in the BIOS advanced features for Windows 8. It boots by disabling a bunch of USB devices for faster boot times, but causes the system not to shut down. Got 5 successful shutdowns in a row so I call it fixed.