You can use your USB/Serial adapter to program the 2560 as the Arduino uses the 16u2 as the same thing to program the mega. You shouldn't remove the 16u2, just wait till you get the programmers and reflash the 16u2 with its firmaware and it will work, I actually had the same problem where the DFU didn't work and the 16u2 stopped responding, after reflashing the firmware it worked. The firmaware can be found under(as of 1.6.0):
You need to connect the Serial pins on the FTDI and Mega in the below fashion:
The Capacitor between the
DTR pin and
RST pin are needed this should be 100nF.
I have bought an I |SP programmer but it will take 3 weeks to reach and no I dont have another arduino, TBH I'm scared to buy another one... – echo_salik
If you are buying clones, those will more than likely give issues as they will be cutting back on costs in places, i.e. QC checks.