Unable to upload Arduino sketch to Arduino Uno using AVR ISP MKII and Ubuntu 12.04
If your Uno's AVR is the 28-pin DIP, the cheapest, quickest, most painless way to fix it is to replace the chip with another boot-loader installed one, available from lots of suppliers.

An FTDI cable (USB-A -> serial TTL) is so easy and convenient to use with your standalone, there's no need to risk your development board.