You've stated yourself: 
"While his skills as a ninja weren't the most impressive among his peers, Akira takes the spot light from his kin due to his ability to host the red chimeran hornets. A dangerous parasitic insect by nature that ravages the body of most organisms it is allowed to infest. Known as the red mist to many other countries, the red chimeran hornets are native to Iwagakure as dangerous pests that devour all who cross them. 

The only other ninja said to have successfully hosted the cruel insects was the First Tsuchikage."

A direct quote. These things are living and breathing. They don't rely on chakra to live, nor do they have a reason to follow your character.

So:
1. How do they communicate? If not pheromones, then what? What keeps them from attacking each other and using each other for their offspring to grow in? The Queen? How does SHE communicate with them?

2: Why exactly does the Queen allow him to control her? Why did she submit, because he gives her chakra?? Why is it HIS chakra? What made him so special? How does HE communicate with HER? 

3: If every other hornet belonging to this species uses a host, why does the Queen need chakra? Does it increase her power or something? 

4: What in the hell are they feeding off of? The Queen is feeding from chakra for whatever reason. Obviously, if these hornets are within him and hatch in him, that means that they have to EAT their way through his body to get out through his pores, right? Does her have some ability that keeps internal bleeding at bay? Super healing that heals the eaten portions right after the nymphs pass? If the queen is the only one that can breed and doesn't fit the breeding pattern of the rest of her subspecies, then why did you mention the breeding rituals of the ones that don't pertain to your character's circumstances?

5: I did read your attacks. They rely on a swarm/horde mentality to attack. You wrote that in yourself. Does your character communicate telepathically with the swarm to use them as an attack? If so, why bother with the Queen? If not, then does that mean that there is a time delay so he can ask the queen's permission? If they communicate, can the queen refuse? Can she even think? Is she unconcerned with passing on her genetic data via breeding? How does she even produce these eggs if all of the drones are, you know, being sacrificed? 
 
You didn't make a species, you made a tool. Well, my character uses the same tool, just be happy I gave you a heads up. 

Just make these things bees. Easy, simple, no problems. Besides, you already have your clan somehow raise them in harmony...when Hornets are natural predators of Bees, but screw logic right?