I'm going to try following this http://arduino.cc/en/Tutorial/ArduinoISP to reflash the firmware with my megas. This post http://www.forums.adafruit.com/viewtopic.php?f=25&t=19438 mentions that on an Uno they've successfully used ISP to bypass the 8u2. I'll see what I can find to test the atmega2560 with ISP. Keep you all posted 