You would presumably need to change the core files that initialize pins that aren't present on your smaller chip, which I think means a new "variant" for the SAM platform. That doesn't sound like something "easy."
I dont have a problem sitting down for an hour or two and manually going through to edit it....but Id just need some pointers on exactly what needs to be modified, and maybe an example for "one" of the pins...then I could just wash/rinse/repeat for the rest of the pin reassignments?
I would be happy to share my modified files once done.