Still got 135 errors but all in USBcore.cpp
But Im able to build I got a libArduinoDueCore.a in my Release folder.
But I think the linker script isnt working for de MyProject
If I build your example I only get a main.o and a syscalls_sam3.o in my release folder..
EDIT
All the errors about USBcore.ccp are could not be resolved errors like:
Field 'UOTGHS_DEVCTRL' could not be resolved