Graynomad:
As for the circuit, you can remove most of the stuff on the Due board and there are a couple of threads running (with example schematics IIRC) about this.
where are these threads?
btw my application needs only digital input and output, and a bluesmirf from sparkfun connected to serial port(14/15 pins).
To rewrite the code i left the usb programming port which i'd like to use even as recharge circuit for the battery: is this possible?