Hi,
For the most part, it is safe to reassign everything but the 'step', 'ST4' and 'serial' pins. For the ST4 there are two locations which are allowed selected by a #define in the pin mappings. For the Step pins, these must stay where they are (less important in the more recent firmware, but better for if I decide to change the code later on). Serial could I support be used with one of the Mega's other UARTs, but that would require changing the serial code (I am using my own as the Arduino one is very inefficient).
The other thing to remember is that you are not allowed to use Digital Pins 30 to 37 inclusive for anything. Make sure these stay unconnected.
One thing to bare in mind is that if you use your own pin assignments, you will have to recompile the code whenever I release a new firmware update as your pin mappings will be different from mine.
Regards,
Tom.