Just as a followup to things, I decided to move from my SSD after it seemed like that was working fine after using it for a few days, but I need actual hard drive space if I'm going to play gamess, dropped that out for the other HDD. Put in the other HDD and started noticing some definite issues with it. Was seeing the C Drive just pinning it at 100%, dropping some, maybe leveling out, but spiking a lot with its performance. So I did the "sfc /scannow" and it didn't find any problems and so I went and did "chkdsk /f /r" and it seemed to calm things down. Don't know if it fixed entirely, but it's not freaking out like it was before and I'm not seeing the same slowdown as before.
Thanks again for the help, gonna see how this goes for now, but hopefully things are fine and I don't need to worry about grabbing a new hard drive any time soon.