Hi Luke
Vladimir say that is better connect miso-mosi-sck of atmel328 with misoout mosiout sckout of bitfury chip. Then write a driver like nf1_init (sorry but in vb.net because it is the language that I know better) and you should translate in C.
About the algorithm that manage the energetic behaviour of device, it should be written in external file "PowerManagementScript" so anyone could change it.
What do you think?