I noticed that some of you had a similar scenario that I experienced where it seemed like no posted solution online helped the problem. I managed to unbrick the mega 2560 by a few steps and two sources that I will provide credit to.
I followed Nick Gammon's guide to flashing both the ATmega 2560 and the 16u2 chips using an Uno through the arduino IDE. Follow his instructions here:
and the source codes are provided on his git page. His programmer can be saved into your sketchbooks
After flashing the 16u2, the USB will be unrecognizable. This is mentioned on Nick Gammon's section about the 16u2. As I was flashing off of Windows 8.1 I instead used Atmel Flip as my dfu programmer http://www.atmel.com/tools/FLIP.aspx.
The "L" led on the mega should be flashing if you're in dfu mode. Disconnect the wires to the Uno if it is. Next I recommend following this youtube video on how to use Flip with the 16u2.
When selecting the hex file to load locate the arduino folder on your C drive (for windows) then go to /hardware/arduino/avr/firmwares/atmegaxxu2/arduino-usbserial and select the Arduino-usbserial-atmega16u2-Mega2560-Rev3.hex file.
Before I did this I flashed the combined file and turns out the address was out of range.
Unplug and plug in the mega after and a new com port should appear in your device manager/IDE