You would have to be careful that your i2c code never blocks, as most uses do by default and that will not work well with the music shield. Outside of that it ought to be doable, but I have not checked the pins carefully. You should be able to pool in the same loop that is polling the software serial port for commands off of the ipod connector. Be sure that you are buffering your input to complete your command before acting on it and getting into a blocking state that wedges the player.