point5:
Using Nick's code below I was able to get down to 400uA with everything unlugged which suggests the rest is down to the board peripherals?
That much could easily be drawn by the voltage regulators, even if you are injecting power downstream from the regulators' output. In addition the RTC spec shows that it draws 100-200uA. The simplest solution for ultra-low power would be a standalone '328 chip. Myself I like to use Sparkfun's Pro-Micro because you don't need a chip socket or PCB, but it requires some minor surgery to cut the trace from the voltage regulator.