I am posting this issue here since I'm reasonably sure that the issue is with my HDD.
So for the past day now, I have been hearing muffled clicks coming from case. It seems to come from behind my two front fans, which is were my HDD is stored. With these clicks comes a noticeable slow down in performance. Start-up time, shut down time, applications stop responding (Firefox), games take much longer to load/don't load at all. I've had 2 errors when booting up, prompting a self repair program. The clicking doesn't happen all the time, but when it does, the drop in performance occurs.
The source/timing of the clicking and the fact that it is a refurbished HDD are my main two reasons for thinking it's HDD related.
If anyone has any helpful suggestions I am more that open to it. If all else fails, I will probably grab a new HDD.
Thanks for the help, and let me know if any additional info is needed.
Okay. Fortunately I don't have a lot on here that isn't easily replaced. Time to start hunting for new drives. Not sure if I want to go SSD for now, then get a data HDD later, or get the HDD now and maybe upgrade in the future.