OK, so at this point you've ruled out GPU drivers from being the culprit. It could still be hardware related (GPU) or problems with that WD Green as mentioned on the last page - or something else.
Suggestions at this point:
1) If you've been testing games on that WD Green, swap them over to your main drive (SSD?) and see if there's a difference. This isn't going to be easy, I know.
2) Based on everything you've already tried, this is fast entering "reformat and reinstall" territory because you could spend weeks trying to figure out what's going on if it is software related in some way. Simple route may be to create an image of your OS drive, then nuke it and reinstall the OS and see how performance is. If it's the same, revert back to the image. That will pretty much tell you if you are dealing with a software or hardware issue, though, if hardware, you won't be sure exactly what just yet.
3) If you don't want to do that, I'd investigate chipset/motherboard drivers next. Did you happen to do a BIOS update at any point in the past few months that may have reverted your SATA controller from AHCI, to say, IDE, forcing the OS to reinstall everything?
