Hello there Jonesie85, that's quite a problem you've got there, and it's very well articulated too!
I'm not an expert but i'll try to answer the questions that i can, as best as i can based on what i know from my limited knowledge...
1a-d My knowledge on the inner workings of the BIOS is limited so i'm afraid i cannot give an honest answer to those questions
2a - 2 additional HDDs by themselves would not AFAIK sip enough power to cause permanent damage to your PSU (based on your system specs, I reckon you have a beefy enough PSU to handle a full rack of HDDs in RAID10 or crossfirex with 2 or 3 graphics cards!)
2b - The only way to find out as an elimination exercise would be to reinstall those drives on your system and repeat the steps (surf the net on firefox and use your torrent software) that caused the issue.. If the issue still persists than you can rule that probability...
2d - Probably so, but have you used other intensive software to rule that out? You mentioned that your system performs admirably when running Skyrim (itself quite the demanding game at high settings), but you didn't mention how long for. To rule out the concidence and to narrow down what the problem is, have you considered stress testing your system with Furmark (www.ozone3d.net/benchmarks/fur/
) and Linx (www.xtremesystems.org/forums/showthread.php?201670-LinX-A-simple-Linpack-interface
) seperately and together?
3a - To put it simply, a damaged graphics card would flatline more sooner on game than on an internet browser like firefox. Managing to run the game over an extended period of time successfully, but failing to do so on a lighter program like firefox would indicate a software problem or the problem is focussed somewhere else (not a GPU issue)
I hope that helps out somewhat.... Sorry if i couldn't be more concise!