Dear Ben
your essay and your ideas go far beyond what one could expect from a purely mathematical training. My best compliments! Getting some things wrong is part of the process at the beginning: better making some starting mistakes, than working unmistakably on a useless program. It is part of the adventure!
Thank you also very much for your appreciation, which I know as sincere, out of academic competitions and twisted routes. Personally I have a strong believe in the value of my quantum automata program: after now 2.5 years that I started this program, it is really keeping all its promises, and you will soon next papers on Physical Review D. It was the same with my previous axiomatization program: it took eight years to develop completely, but now it is closed with the Physical Review A published with Giulio Chiribella Paolo Perinotti, which got a Viewpoint and quite a recognition around. If I now have decided to involve full-time three collaborators of mine, it means that I'm working seriously to it (and we are doing it currently with no funding, using some remaining overheads).
Now, coming to your questions, which also help me clarifying my ideas when talking to others.
The quantum automaton that I mean is a unitary evolution that is translationally invariant and local in the sense of Werner and Schumacher. To be more mathematically precise the evolution is an isomorphism of a von Neumann algebra, but here we really don't need such precise definition, since in the spirit of Deutsch-Church-Turing thesis we consider only states that have finite support over a locally invariant vacuum, whence we need to evaluate only evolutions in the causal cone, which for finite number of steps is finite (many people call these evolutions "quantum random walks", corresponding to finite numbers of particles in quantum field theory). Thus the lattice is obviously infinite, due to translation invariance. Translation invariance must not be regarded in a metric space, but more precisely as topological homogeneity. Locality means that a finite-dimensional algebra of a single system goes to the linear combination of the algebras of a finite number of next neighbor systems. This is a causal structure of topological nature only, no metric: there is just a simple rule that connects one system to other two (or few) system and so on, making a network. For a mathematician: an Alexandrov topology. The causality of Quantum Theory (first axiom!) gives the order relation. But there is something more than pure abstract causality: the quantum nature of the causal relation. So, in terms of cells, edges, and nodes: the cells are finite sets of finite-dimensional quantum systems, e.g. two qubits in the case of Dirac automaton. The edges are the causal connections and the nodes are unitary interactions between two (or few) quantum systems. Causal connections and quantum systems are the same thing: the cell is just a finite set of them. As an example, take just a simple homogeneous quantum network, i.e. a quantum computer, where infinitely many qubits are connected only through bipartite gates in a brick-wall way. See e.g. figures in my previous FQXi essay. In my case the systems are described by a complex operator in an infinite dimensional Hilbert space (but the algebra locally is finite dimensional!), corresponding to the field labelled by lattice points. The most synthetic and elementary mathematical definition of the automaton is now just a finite matrix (4x4 in the Dirac case) where elements can be just multiplication of the field in a cell by a scalar and operators shifting to next neighbor cells. All coefficients are constant, corresponding to homogeneity of the automaton. The matrix is "unitary", in the sense that it preserves the scalar product between any two states with finite support. That's all!
Regarding your last question, I'm not sure I understand it, but I think that the answer is positive in the sense that if I take an abstract causal network (call this "classical"), namely an (unbounded) graph with no loop, describing a partial ordering, I can associate a unitary interaction to each node and a quantum system to each edge.
Thank you again for your questions. It is very helpful for me to answer questions they are genuinely motivated by the understanding, as yours. It helps me a lot in making my ideas clearer, and affects next scientific writings.
With my best wishes for a career as a natural scientist, not a technician of any technique ...
Mauro