Problems deriving state diagrams
You should only consider drawing the state machine for the actual 2-complementer with serial input, and forget about the shift register (drawing a state diagram for a shift register of a given length is perfectly possible, but makes hardly any sense). 

Said that, the task boils down to a single-input/single-output state machine with 2 states. Look here: http://k5rec.blogspot.com/2006/12/digital-electronics-serial-twos.html