Fortunately, I have resolved this very scary problem. It was simply solved by updating the BIOS, which I would have tried much earlier if it weren't for a bad experience I had with flashing a BIOS 20 years ago.
The original BIOS version on mine was 0404, which is apparently incredibly old. In fact, on the Asus websit they call 0505 the "first release" and mysteriously they claim it is the oldest version which even supports the Haswell-E CPU's (obviously, that makes no sense, but that's what they say).
The first time I loaded up the new BIOS all my problems were completely gone. Pressing delete or F2 let me load it regardless of what USB port the keyboard was in, and when everything was set the default "auto" settings, it actually put everything to factory spec, which I had to do manually before.
Also, Windows loaded no problem. I'm using the machine to type this right now. Everything looks great.
God, that was scary.