Has anybody tried something similar?
Yes. It works fine.
I am also guessing I would leave this in here to keep the USB enabled, but where to add the above code to read Pins 2,13? Right after it?
If you are not using the Serial object, then you don't have to leave that in there. If you are, you do.
The code to read the mySerial (lousy name; what is wrong with xbee?) instance can go before or after that BLOCK of code (that you don't show all of).