When I remove the AtMega644/1284 and the stepsticks, I measure 6mA on the 13.9V input. How much you get?
I still wonder if the problem is not due to some short (to GND or 5V) of an output pin of the AtMega...
I still wonder if the problem is not due to some short (to GND or 5V) of an output pin of the AtMega...