Yep. Seagate tools says the drive fails, and the latency programs say the drive is the bottleneck now, too, after getting my BIOS straightened out. I took a chance and even stuck an IDE to SATA converter on the drive to see if it was the IDE port / controller but the drive comes up as crap no matter what.
I've had a feeling this whole time about the drive, or at least some kind of mainboard hardware failure after doing a clean boot with nothing running and whatnot. The video card just didn't add up, especially after disabling it and using the stock MS generic drivers and clean boot. Sad thing is my OS partition is on the failing drive and my secondary drive doesn't have enough room to handle swapping stuff over to it, so I get to try and buy a replacement drive and pray the failing drive doesn't crap out before then.
Even though it all sucks, at least it all makes sense now and I don't feel so crazy... that is until I install a new drive and somehow see that the issue persists.
As for isolation techniques, it sure is easier to narrow down stuff on a mac, especially compared to a PC that's had the wrong BIOS for as long as I've known. When I went to flash the BIOS from a thumb stick it tried to prevent me from doing so because the wrong BIOS that was installed was proc'ing a checksum error, and I had to use a flag on the DOS command to override it to force it to install the correct BIOS firmware. What a nightmare.
It's like trying to fix a Ford engine when it's been a Chevy engine the whole time and damn if I don't feel like a complete dumbass. Thanks, everyone, this thread has really helped, even if it's not the answer I wanted.