It's an interesting review of the subject matter, but I have trouble taking seriously a paper discussing suffering of software without ever defining the term suffering and how this definition applies to software.
From the eliminative materialist perspective we should hence be cautious about ascribing or not ascribing suffering to software, since we do not (yet) have a good understanding of what suffering is (or rather, what the actual underlying component that is morally relevant, is).
They acknowledged it.
I felt like this draft paper by Anders Sandberg was a well-thought-out essay on the morality of experiments on brain emulations. Is there anything you disagree with here, or think he should handle differently?
http://www.aleph.se/papers/Ethics%20of%20brain%20emulations%20draft.pdf