Nick, can you shed some light on trying to repair a R2 MEGA2560, I'm still getting weird signals from one I accidentally bricked a few months back, and I managed to re-write the bootloader using an UNO as the ISP, and, despite it ending with an error, the MEGA still worked, But it's still wonky talking to a Linux laptop. (Sometimes, It starts talking right off the bat, other times, it needs to be disconnected/reconnected before it will accept code from the laptop.) (Running IDE 1.6.4, under Ubuntu 13.04)
Try the loop-back test, you may have damaged the USB interface chip.
If you get hold of an FTDI cable, and use that for the USB interface (temporarily anyway) that would eliminate the USB chip as the cause. You just have to wire up Vcc, Gnd, Tx and Rx. The RTS pin isn't required if you aren't trying to program the board through it.
@gelfling6, please try to refrain from hijacking.