I've just restarted my machine and my HWID has infact just changed once again.
All my hard drives seem to be in good health based on running CMD with the command "wmic diskdrive". Though, I did have 2 external hard drives plugged in to my PC for a few reboots now. I unplugged them yesterday and restarted my PC today, which is when the HWID changed. I'm unsure if that's related in anyway whatsoever, guess that's something I'll be testing after work.
As for the clean boot, I did make sure to tick to hide all of my Microsoft services (I actually want my PC to run correctly when it turns on after all).
I will take your suggestion and turn half on and half off at a time, but ultimately it seems unlikely.
I have never used a HWID Spoofer before, only considered one because of my situation. I can now with absolute certainty confirm that I have 4 different HWIDs on this machine and it's driving me insane.
Edit: I've just replugged both external hard drives in and did a restart. My HWID changed once again. When I get home I'll restart the machine with the hard drives in a few times and see if it changes... If it doesn't I'll unplug one and then plug the other back in and unplug the other to see what it changes into... This is absolutely insane and makes me question why I haven't just done a format already and just forked out for a Windows License.