The good news is, I believe the 2560 and 1280 are pin compatible, but here's the issue. As far as I know, its not possible to source a 2560 with the arduino bootloader pre-installed. Thus, you will have to find a way to flash it with the new 2560 bootloader. This should be possible (you can do it with the atmega328), but it will probably be a pain. Lastly, the 2560 bootloader is meant to be programmed from the atmega8u2, but by the schematic, I think it should still be able to be programmed by the ftdi chip (its all just over TTL serial).
I think you already know this, but soldering TQFP is a real pain...maybe just grab a new mega. Besides, at least in my opinion, the best feature of the new mega isnt the new proc but the atmega8u2 instead of FTDI, which you will be stuck with on the 1280 board. It really doesn't seem worth it.
Good luck!