Maybe I missed where the max is 5v.
The Atmega328 Datasheet clearly says that all I/O pins have a Max Voltage of VCC+0.5v. The Arduino documentation could probably be clearer on this point. You are right, the reason for ARef is for anything other than the internal 1.1V or VCC as the reference.
I don't know what the 8U2 is, but it sounds like that's probably what I fried, then. I'm guessing this means I'lll just need to get a whole new board?
The 8U2 is the other microprocessor on the Uno. It is the surface mount component near the USB port. It handles the USB/Serial communication between the PC and the ATmega328. Unless you can do the rework yourself, you'll need to purchase another Uno.