Something is wrong with my Arduino Mega 2560 R3. The Serial port option in the IDE is greyed out all of the time and the computer detecting anything when I connect it via USB. I did some research and found out it might be the fault of the 16U2 chip drivers. So I need to use flip and go into DFU mode to fix the problem. Only problem is I can't find any clear instructions. The one on the Arduino website is for the R2 version. THe R3 is a bit different and I'm not sure how to proceed. Please help 
I have the exact same problem. I'm trying to use the guide here but when I try putting the mega 2560 into DFU mode I get the error:
dfu-programmer atmega16u2 erase
dfu-programmer: no device present.
make: *** [dfu] Error 1
I assume this means that I didn't get the Arduino properly into dfu mode