Based on that conversation between Sora and the VP, I think Sora actually committed suicide by somehow inhabiting some other person or putting that person in a trance to make him/her/them kill him. Perhaps it's because of those snakelike eyes Sora periodically has.
Going along Smokron's train of thought, I think that maybe the "brain" of the automaton is patterned off of his father. So, in other for the mind upload to work, perhaps someone with a similar personality/thought pattern was required to pilot it.