Just an update:
I completed everything and eventually reinstalled windows. I used a HD scanner from the manufacturer's website and performed a long scan and it passed. However,
this morning, I got an error stating my computer couldn't come out of hibernation with an error code (don't know off the top of my head). I ended up rebooting and everything seemed fine.
Is this independent to my HD issues or is it a common problem? And is there another HD scanner I can use to double check if my HD is ok?