Virus persists through Format
So... I have never run into this before, but I'm suspecting "the crap" is actually tied to his Microsoft account. I suspect this because the one time it did work, I just threw together a dummy account/email while he was out of the room and everything ran fine, even after a few restarts. Logging him in his own account loads "the crap" and then results in the crash and missing sys32 file. This explains why it wouldn't recur in some situations as I would get him to log into his own account.
How would I go about remedying this?
When you install Windows 8, it asks you if you want to port the backup/sync account from a system. Listed are the current system, and any other Windows 8 system using the same account (say: laptop, or tablet running Windows 8).
It is important to select that you want to start fresh and not sync old settings.
Windows 8 by default syncs:
-> OneDrive folder
-> Windows end-user GUI level settings
-> Themes
-> IE (It's like Chrome or Firefox sync. It will sync addons, bookmarks, open tabs, and history)
-> Wireless Passwords used
-> Apps installs, and purchases, including in-app purchases
-> Accessibility options
-> System Language settings
Under PC Settings > OneDrive > Sync Settings, you can customize what you want to sync or not, and if you want to make a backup of settings online (for re-installs or transfer of systems)
Sorry for not catching your thread before. I was particularly busy with school.

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