Installed into a new partition, If I recall correctly, but I am not 100% sure. I think I manually deleted old system files, and did a couple of registry checks. I didn't back up the last time I was at a stable condition, so I'd probably have to transfer the most important data onto another drive, and then do a complete reformat, and reinstall back onto either of the hard drives.  I was just really hoping to avoid the hassle. Might have to though... :/

I think some of my problems point to a faulty hard drive (longer load times and such), but I was hoping maybe there was a bottleneck somewhere that was causing problems all around. I am not entirely sure, but I just bought a third hard drive on newegg. I'll attempt to RMA this current hard drive, and send it in once the new one comes in. God, I hope this makes things smoother.