As much as I know you want to just make this work, simply repair the board properly, replace the 2560 if it was damaged.
Running alternate firmware and rigging the board sets you up for a lifetime that now when new updates come out, you have to compile from source, make your mods just to keep up.
Yes, contact Makerbot and see what they say.
I do it all the time, tell them you want to order the board. Sure it will take some time through the menus and see what they say. Be warned for some sticker shock.
If you don't buy the board (and trust me, when you hear the price you might lose it), maybe, maybe someone there feels sorry and helps you out.
Again, worth a shot.
https://www.makerbot.com/contact-us/Otherwise, replace the 2560. It can be done, I've done a fair amount of boards by hand with nothing more than a good soldering iron. I even remove the old chip using a penny for heat with a big soldering gun to remove the old chip. Whole process is maybe 20 minutes.
I would offer to fix it for you but I'm traveling for the Holidays and unlikely to be able to do it for a few weeks.