Any chance of repairing Mega 2560?
http://altlab.org/d/m/jpralves/recover_atmega2560/

Change fuses/firmware depending on which side you are flashing (M2560/M16U2)

Firmwares: Arduino-COMBINED-dfu-usbserial-atmega16u2-Mega2560-Rev3.hex / stk500boot_v2_mega2560.hex

1st command: 

avrdude -C avrdude.conf -P usb -p m16U2 -b 57600 -c usbtiny -U lfuse:w:0xFF:m -U hfuse:w:0xD9:m -U efuse:w:0xF4:m -U lock:w:0x0F:m


2nd command:

avrdude -c usbtiny -p m16U2 -P usb -b 115200 -V -U flash:w:Arduino-COMBINED-dfu-usbserial-atmega16u2-Mega2560-Rev3.hex


3rd command:

avrdude -c usbtiny -p m16U2 -P usb -b 115200 -U lock:w:0x0F:m


http://pastebin.ca/3178420