Well, I've decided to go about reinstalling Windows today, it's been kind of slow and hard disk space is slowly running out. I spent the day yesterday deleting old files I will never use anymore, and archiving a few old folders I probably won't access for a long time. I freed up over 35 GB of space on my file storage drive, and at least 5 GB on my Windows drive, but 18 GB is not a lot of free space ;)
Not only is the hard disk space an issue for me, but a few months ago when I last reinstalled I caught come malware and it proceeded to delete all the shortcuts from my Start Menu. Also after than, sfc /scannow refused to do anything, so I'm sure it went deeper.
Going to load Windows 7 on my USB drive and reinstall, after that's done and my programs are back on I may reinstall Ubuntu afterwards, not sure yet. I just got done backing up my Steam apps, so it's off to format I go!