If you're only using Arduino-library calls, code should compile between the two. However, many libraries that are designed for the AVR-core chips address specific registers that may not exist in the ARM-core chips.
My guess is that you're running into register conflicts.
I doubt there is a "reference" or "guide" comparing the two in detail. It would basically come down to comparing the two processor's datasheets. You need to evaluate each part of the code that isn't compiling and determine if there is equivalent hardware on the Due. (or see if the libraries have ARM/Due specific versions.)
Lastly, don't forget, I/O voltage difference between the two boards.