@Jarek feel youre overthinking this. you have a physics phd right? its useful but also interferes with "beginners mind". have you done any cellular automata research? heard of wolfram? how about conways life? there is a concept called "gliders". particles are likely 3d "gliders" and suspect different "sizes" are persistent/ possible. its more a matter of experimenting with simple 3d CA rules which will locally look somewhat like E/M or wave propagation eqns.
However, to "uncompute" the auxiliary qubits, he starts with " duplicate the input bits ", what seems forbidden by no-cloning thm, there is no gate which takes one qubit and produces its two copies ... ?