I find these kinds of arguments to be semantic tricks. These are similar to proofs that claim 1==0 or some such nonsense. The examples basically subdivide the operations so far that you are looking at individual atoms in a structure or letters in a message and not considering the whole.
Basically, the flaw in the sub-divided brain example are these:
Such a brain is not perceiving anything. Its neurons are not communicating. It is not having sequential thoughts that flow from one to another. Non sequiturs could be programmed just as easily. If the humans make an error in calculation and program someone else's brain pattern, it would go into this scheme just as well as the original brain's.
Basically, the humans are slowly modeling a brain's activity on paper. Rather than the brain functioning on its own, and the humans seeing the activity, it is the reverse. The humans are determining the activity, and then pretending that the brain is functioning thusly.
It is a trick to explain this to such a level of minutia that people become confused as to whether the brain really is still functional. This is an argumentative trick that prevents objections from properly being addressed. The brain is obviously dismembered and not functioning. It is an elaborate puppet that is made to do what the very large committee of puppeteers scripts it to do. Nothing more, nothing less.
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