Shorted - "Otherwise IF you have a shorted MOBO: unscrew both the MOBO and PCIe, pull away from anything conductive and supported by a towel - test. Also pull the USB headers. Including re-installation of Stock HSF." Test.
First, I have no idea IF your MOBO is indeed shorted. Often USB issues are indicative of a short either by the Standoffs, I/O, Case headers, peripherals, etc. I'm trying to help you 'isolate' the issue(s) as best as possible. Guessing helps no one. I can see the KB/Mouse is cheap and it's not unheard of that some KB/Mice don't allow BIOS control. I use good equipment that I know works including PS/2 devices.
You can borrow someone's KB/Mouse or purchase new. IF a new 'good' KB/mouse fails then first look carefully for a short, including doing a Breadboard {MOBO on a piece of cardboard with minimal connections}. IF the Breadboard fails with use of new KB/Mouse then sure the MOBO might be 'bad.'