Alright, so, I just pried out the extra HD after yet another crash and toyed around with my PC for a bit to see if it was going to go crazy on me.
The first reboot immediately after removing it got me a crash, but a different kind. Basically it was like my PC got immensely busy while starting up all the stuff that starts up at launch(One of my IM clients, firewall, GMail notifier, AV software, necessities like that) and one by one, things just stopped responding, starting with my start menu/task bar. "Okay", I thought, "Computers can be wacky, let's try another reboot." Started up fine, no issues, thought I'd put it to the test right away so I fired up Call of Pripyat and played for two hours with no issues.
But it's given me periods of peace longer than that before, I suppose time will tell whether I need to post another tearful plea for assistance or not. =P