Back to the board that set fire. You should have RMA'd when the 8-pin stopped working first and foremost. But having USB issues as well just sounds like it was a lemon. You should have RMA'd already. The 4-pin is auxiliary power, because it says this in the manual, ASUS might not accept your RMA now because of user error. However, you should still fill out a support ticket and before they even respond call them.
On the topic of RMA's. I have RMA'd motherboards with ASUS twice, motherboard with Gigabyte one, GPU with EVGA last week, and even a mobo with Biostar. All of them were taken care of in two weeks or less, EVGA was the best, I had a new GPU shipped to me 2 day shipping in advance.
Biostar sent me back the same board unfixed, so I sent it back again, then they sent me a board with the RAM slot working again but the USB was messed up. It was a $60 AMD board, I had already spent $40 shipping it to them twice so I just gave up on it and as a result will never buy a Biostar product again.
That being said, ASUS, Giga, and EVGA were great. But as I advised burnt cap Crosshair dude at the beginning of my post, call them. Explain your situation, but more importantly, assert yourself as being knowledgeable as a PC enthusiast. They will take care of you, they don't want you to have a bad experience. They just have to be thorough because of all the noobs out there messing up products and claiming they don't know what happened to it. If you explain in detail, it expedites the process for both parties.