I can't find the threads and the search is useless, there have been 2 I think, you'll just have to trawl through the Due board.
i left the usb programming port
By the "programming port" you mean just the USB socket, no electronics?
recharge circuit for the battery
What battery, we know nothing about the circuit. If it's a car battery no, a coin cell probably.
did not need an external crystal instead.
You can use the internal oscillator I think but you'll have to change the system init code, I doubt the standard Arduino version will work.