I would recommend (if you haven't) checking temps/voltages on your components with hwmonitor.
From what I understand, Prime95 is a good way of checking CPU functionality, but I've never done so myself.
Do you have any non-standard components in your PC, such as a sound card, some weird USB devices, etc (anything out of the ordinary that requires a drivers download, especially a non-whql driver)?
If you suspect your GPU at all, you may wish to try running using intel graphics to see if you see an improvement; I really don't suspect the GPU/drivers based on your description and what you've tried, but it's worth a try.
Lastly, you should get the latest mobo drivers for your PC, update the BIOS, and restore fail-safe default in your bios settings. If your still having problems at that point, I would conclude that the mobo is the likely culprit.