I'm writing a scifi story about a human undergoing rapid evolution due to his being repeatedly "connected" to an alien biological machine,that would be controlling the evolution through some kind of program.
Since individual organisms can not evolve, at least in any technical sense of the word that I am aware of, it already appears that you are not terribly concerned with scientific accuracy. It makes no sense to refer to the evolution of a single animal because evolution by definition functions through natural selection and natural selection can not occur within a single animal. I suppose you could hypothesize that neurons are being "selected for" within the brain but even this makes little sense and is not evolution as it is understood today.
Without differing statistical survival of multiple organisms possessing slightly different genomes, the process of evolution can not occur.
one of the changes would be a "master" cell that was able to regulate clusters of neurons from a distance. It would be able to selectively "turn off" other neurons in the brain through a targeted electromagnetic pulse. The idea is that it would act like transcranial magnetic stimulation only far more sophisticated. Leading to far more complex interactions between the cells.
I am going to address this point from a biology perspective (not an electromagnetism physics perspective) but before I do I will summarize right away: do whatever you like as long as you don't break any laws of thermodynamics, because predicting the distant technological future is basically NEVER going to be plausible.
Even more so than manmade technology, it is EXTREMELY UNLIKELY to IMPOSSIBLE to speak seriously about predicting evolutionary progress. What I mean by this is simple and can be explained in two points.
1. If you currently used the most sophisticated engineering known to man today and invested all resources, money, and minds on the planet into achieving the objective of, for example, creating an artificial brain, you would fail, and you would fail HARD. Without using pre-existing materials and blueprints and equipment (DNA, cells, and a womb) we still cannot even duplicate something we have billions of copies to work from. Eventually this WILL change, but my point is that our current ignorance of biology is astounding.
2. I can not think of a single case where a cursory glance at a knee joint or an elbow or a retina or ANY evolved structure in ANY species revealed inefficient functionality for the environment the organism was in. Certainly genetic engineering has worked in the sense that we can predict what environment or properties will be desirable FOR HUMANS and try to nudge organisms in that direction using pre-existing evolved structures, but we have never produced a "superior version" of something that evolved naturally FOR THE SAME PURPOSE. We have forced selection of plants that are better at feeding us and cows that are better at producing milk but we have NEVER encountered any such species that NATURALLY evolved for this purpose. We have never produced a plant or animal BETTER at surviving on its own and that is because evolution is VASTLY SUPERIOR at such things. Our entire ability to think and have a functioning brain is precisely the result of evolution laying down the law and saying, through statistical dominance of various changes, "homo sapien brains are so far the best possible for keeping a reproducing animal alive." We are completely unable to grasp how to improve on current designs precisely BECAUSE of our ignorance and complete lack of experience in this area.
Taking the above points together, what I'm trying to say is this:
You have to have some balls to say that neurotransmitters are going to be replaced. You have to have some balls to say ANY given thing you can think of will "[lead] to far more complex interactions between the cells" when we do not even currently understand how complex interactions between cells are. Cells are powered by energy, not a "voltage gradient," and require a dizzying array of astronomically complex molecules and physics to achieve their proper signaling patterns. They are hardly just wires or magnets with a voltage supply. To think that you can imagine at a detailed scientific level how to create something better than the most advanced structure produced from billions of years of evolution is ballsy.
You may be right, but you may be laughably wrong, and this will be true regardless of how rigorous or physically possible any particular process you seek to describe is. Currently there is no way to answer a question such as "what will a more evolved human brain be like?" even assuming you had all the parameters of the future environment.