Hi
Well, since you do not have any contact with you main pcb using usb, I'll think the Atmel Mega 16U2 is the one to work out first.
There is a special reset point on the pcb just to reset this microprocessor and this is jumper named JP2. There is a little problem here because there is not soldered in pins at this point, there is just two solder points. By shorting this two points, the microprocessor go into DFU mode (direct firmware upload). By fixing this, you should be able to reload (DFU) the firmware to "Mega 2560" for your printer. But ofc. that is true if all the hardwa