Well, I'm going to have to be unfair and say that I don't feel like reading a 100+ page paper in order to critique it unless I'm going to get a publication out of it. So I'm working from incomplete data here.
In those three links, it seemed that PZ's main complaints were about the scanning process, but the responses were about emulation issues, which come up after
a successful scan. Since we're talking tech two centuries hence, it's all wild speculation... so my speculation is that entropppy is going to be a more difficult opponent than it's being credited with.
First off, scanning a dead brain seems pointless: physical processes are probably already breaking down the data storage before you get the thing frozen (water crystallization from freezing also damages things). Scanning a live brain is unlikely to work unless you can somehow take a snapshot of the whole system at a particular instant; even unconscious or under anaesthesia, the brain is constantly changing its state.
Second, dismissing concerns related to the difference between axon signaling speed and electromagnetic wave speed in copper seems to be rather optimistic. There's a level of care that is needed in designing a computational system such that it can run at the fastest allowable speed without generating incorrect results; look up asynchronous computing. And bear in mind that even though asynchronous computing has been around a long time, nobody uses it, because synchronous (clock-driven) computing is just so much easier to deal with. Correct operation can't be trivialized either; it's the whole point. Further, due to signaling times, the brain can create timings and synchronization that may not replicate in a simulation unless it is run at the same speed as the axons.
Third, the interface to the outside world is going to take some serious mapping. But let's assume that one gets whipped. If you can scan a brain, you can probably map the neurons in the optic nerve. If you don't get it right, everything is going to look wrong and you won't be sure why.
Fourth, if anything fails, you die. I really haven't seen much consideration for failure recovery in any of these discussions.
I've found that I really can't take the singularity stuff any more seriously than discussions of Star Trek
physics. A fun diversion, but not really very likely.