Alright, the problem has been addressed. Swapped in my buddy'* MSI KT3 Ultra-ARU board a few days ago, then wiped my hard drive clean and started fresh. Running much better now.
Interesting note: The BSoDs were caused not by my hard drive or mobo, but by two sticks of his RAM we put in the system. We thought they were good, and they turned out to be crap. So I don't think it was necessary to swap my board out (though at least four of my capacitors look swollen/leaky). Still, I won't be going back to my board because of the capacitors, and because even at 4x AGP I'm benchmarking just as well as the old board, processor, and hard drive setup.
New question: When I install Nvidia NTune on this machine to overclock the video card, it doesn't retrieve the proper system information from the motherboard. Fuzzy Logic has the same problem, and because of it the GPU clock frequencies are not reported, meaning I can't change the clock frequencies. Any idea why this would be? Here'* a screenshot of the system information within NTune for reference.