I'm not sure if symbiosis from a true mutualistic perspective with a virus is possible, as viruses are natural intracelular parasites, but other than that it's not that bad. Your pathogen seems to be closer to a bacteria, and one capable of editing human DNA.
Regarding the changes in the body. Enhanced vision and hearing can be achieved mostly by a higher number of cells responsible for these activities. Considering we have birds with smaller eyes but higher cone density, it's not impossible.
Considering the muscles, you could maybe increase muscle density and reduce a little the layer of fat, but a significant increase will need additional muscle mass. To make that addition as small as possible, your pathogen could be modifying the bones' internal structure to strengthen them (maybe remaking links or incorporating particles to strengthen it, though it can't be truly unbreakable, that's impossible), as well as reducing some of the natural limiters your body imposes to your muscles (we're actually much stronger than what one usually sees, but it's precisely because using such strength is both tiring and potentially harmful that our brains limit it. There are several cases of people with tetanus breaking their own bones during the violent muscular contractions the disease is known for, and your mandibles on a daily basis can bite a finger off).
Regarding the mutations from the eaten zombie, I don't think so, at least not by eating. You said that the pathogen can force the body to develop different adaptations, but for that the pathogen needs information. Digesting the mutant will break down his precious genome and with it, it's ability. If instead of eating your character absorbs a part of it, we could have something similar to what happens in bacteria, with one sharing a beneficial mutation with others through the use of plasmids, except in here the plasmid would be a bit of the other zombie's body, whose genome is analyzed and broken down so the pathogen gets the info it needs to apply the mutation to the boy's body.
So, can the scenario you want happen? By going 100% into the real world logic? "No". It's not that it's truly impossible, but it wouldn't be like you described, and would take much longer periods to happen. However, taking science in a bit looser way and with a tad of sci-fi logic, yeah everything you want to implement is more or less doable, given it has in ways real-life examples (although usually on a smaller scale and taking more time to happen).