Ahah, Interesting...
So after I rebooted after installing the GPU drivers, I seemingly got the same thing as earlier. (Black screen, then windows background but no windows, etc.)
However, this time I was able to move my mouse and see the cursor.
The screen then darkened a bit, and ~3 minutes later it went back to it's normal brightness.
After it did nothing for five minutes I restarted my PC and went into BIOS to change the primary graphics adapter to PCI-E from onboard (not sure if this had anything to do with it)
It then booted windows normally and it's been running stable for about 10 minutes now.
So I guess my issues were caused by a number of things:
1. The sata controller (apparently) caused the HDD to disappear from BIOS/disconnect entirely.
2. An update installed through windows update causes my PC not to want to boot windows anymore, this I fixed simply by not installing any updates.
3. Primary graphics adapter had to be set to PCI-E after installing GPU drivers to fix the 'windows background but no windows' issue.
I'm going to see if it stays stable or not and if it doesn't I'll check in here again.
I'll mark this thread as solved for now.
Thanks for your help and time guys, I really appreciate it