1) Buy the Windows 8.1 64-bit OEM disc (roughly $90 through pcpartpicker)
2) Use the Microsoft tool to create a USB stick if you don't have a DVD drive (done on another PC of course):
http://windows.microsoft.com/en-CA/windows-8/create-reset-refresh-media
3) Before installing, make sure to backup any data you need and do a fresh install. It's possible to keep data, but you can't keep any programs. I suggest just copying any data to a USB drive, then simply DELETE the entire partition on installation start so you're doing a complete install
4) After Windows 8.1 installs, there may be an "OLD_C" folder taking up space. You can delete that. Google for how.
5) Install drivers, programs etc. (main chipset driver, video driver etc)
6) Use Acronis True Image or a similar tool later to create a BACKUP IMAGE so you can restore it in case of problems. Periodically make a new one.