The only reason Naruto could get to Mid-High A rank is the fact that he absorbs memories. It is the experiences and the muscle memory that really does the upgrading. Add that to a Super Genius and it is possible. Naruto has the gift of innate understanding. He is able to break something down and improve it in all fields. As for abilities he takes the most potent ability. If that is a Bloodline then he gets that. However like the Toru he can get skills. In Toru's case it was Chakra Control.
As for a Mutation, kind of. With Chakra changing based off of your personality it would have to change your body over time. That is how Kekkei Genkai work, some people in a group have a natural skill for something. Over the generations it becomes a Bloodline.

2 years later

In the past two years a lot had happened. His choice to act as an Informant for Orochimaru was a perfect choice. It had really bore fruit. He could continue his plot to end the leaf. It was awesome really. He had taken to sending a heavily Seal covered, Chakra reinforced Water clone to the Academy so he could train all day. It had really shown. He had grown immensely in that time.

It was though Partially due to the fact that Kabuto had taken to training and sparing with him every day that he did not have missions or Hospital duty, or providing him with Scrolls to train with. This provided Naruto with much needed Experience. It had helped him to grow from Mid-High A Rank to a solid Mid S Rank ninja, with S or even SS rank Skills in all fields. Kabuto himself had been surprised at this.

With Kabuto's help Naruto Had become a master medic around Kabuto's level. Though Kabuto was still better as he had done surgeries and the like but still Naruto and him were equal Battle Medics. By adding the Chakra scalpel, Kabuto's signature, Naruto had turned his Taijutsu Extremely deadly. By inserting his chakra scalpels into the body like a gentle fist Naruto could take down nearly any enemy.

Overall Kabuto proved to be an incredible teacher so Naruto did not have to lie if he was asked about that. It was actually these teachings that helped Naruto to Master his water and Lightning techniques. He used this knowledge to actually control the elements that are in the human body.

Or use his advanced control over the other elements. Though they were lesser when compared to his Water and Lightning control.

As for his emotion sensing abilities, after siphoning a Yamanaka he killed, Naruto was able to read minds full out. It was so useful as he was able to implant suggestions with his abilities. It also helped him to be able to talk to his clones from huge distances and that helped to build his spy network. He was also able to Organize his mindscape further increasing his already massive intelligence and memory. Along with one other, hidden ability.

He loved all his New abilities. They had so many possibilities.

After a rough spar Naruto and an Exhausted Kabuto sat down " Naruto I have a new mission for you."

Naruto perked up. Aside from spying he had been asked to kill specific shinobi and civilians over the years. This would be his first more public mission.

" I Know that you plan on getting on Sasuke Uchiha's team. What your mission is to basically rile him up. Get him jealous, make him believe that he is below you, the dead last. We need him very vulnerable. Also we will need information about your team. All of the. Even of your covers."

Naruto rose an eyebrow." I see so the boy will be his new body. I figured as Much. Those Eyes I gave him back then will be useful if he actually gets the boy's body. "

Kabuto Nodded , though he was not shocked that the boy knew that. He had perfected his information network over the years. After all if he could rig seals to give him all of Danzo's, Hiruzen's, the clan's, and The councils data then finding out information about Orochimaru would be child's play. After it is what he was there for.

" Good. Now Shouldn't you get to bed? You have your graduation tomorrow."

Naruto Rolled his eyes. " Yeah ,yeah. " Rolling his eyes Naruto got up and left, after flipping off Kabuto of course. The grey haired boy just laughed at him.

Kabuto smiled as the boy left. He really like Naruto, even cared for the boy. He loved to teach him, or just to spar. Kabuto had gotten out of the rut in his skills by fighting Naruto. Now he was a S- Rank Ninja. Not just a High A Rank one. Naruto had helped him to grow quite a bit. All of his skills were heightened and now varied. His medical skills had gotten so good after some of Naruto's suggestions he was able to heal Kimmimaro, who also had loyalty to Naruto now.

He had to say that if it came between Naruto and Orochimaru he would chose the Boy. He was his best friend, his brother and maybe someday his master. He had, as always, felt the extreme desire to submit to Naruto. It was Odd but he was okay with him as he helped Kabuto so much.

Kabuto never saw the clone of Naruto hiding behind a genjutsu smirking at the intimate change in Kabuto's Loyalty. This was very good. And that bit about Kimmimaro was very pleasing. But it would not be good if The Snake knew of it just yet. Naruto planted that suggestion into Kabuto then left the field to tell the original.

The Next morning found Naruto Wearing his real clothes finally. He was wearing a dark grey shirt, black shorts and a black vest. He also had red streaks in his hair. They were natural actually, apparently from his Uzumaki Heritage. Naruto was ready to shake shit up.

As soon as he got to the academy, unnoticed, he placed a Genjutsu over himself. He did not want to deal with their stupidity. Of them all only three teams had even the slimmest chance of passing. All of them containing clans. In fact only Sakura was not Ninja clan Heir. It was so sad, they were shunting so much talent. Look at Jiraiya or Minato. Neither were from clans and both are legends. Hell look at Kabuto who was extremely skilled and he had no shinobi linage. The same could be said about Guy, Killer Bee and Yugito the Vessel of the Eight and two tails respectively. All of them were Civilian borns and extremely skilled. It really made little sense to him that the villages would rely so much on the clans. Sure they were good but that made them predictable, their skills so well known. It also makes them weak. With a little study you could eliminate all of the Village in a few minutes.

Naruto already figured out all of their weaknesses. They were so glaringly obvious. Stink bombs for the Inuzuka, Bug repellant for the Aburame, Speed for the Akamichi, Chakra pulses or Armor for the Hyuuga, Basic Mental defenses for the Yamanaka, Strength and speed for the Nara. It was easy to play with them., At least some like the Sarutobi had varying skills. Hell his own clan had Seals, Sword play, water and wind Jutsus, incredible Taijutsu and more. They never relied on one ability. It was so pathetic that others were such one trick ponies.

Really if they decided to diversify a little then the village would be at least twenty times stronger. He could think of ways to turn all of them, bar Kiba and Choji, into S rank or Higher. Really people wondered why there never have been an S-rank member out of their clans. High A is the highest that has ever come from any of them. It was rather sad in his eyes, such a waste.

Naruto had to shake his head to get out of his thoughts. After all they would all be dead or worse in the future due to their own foolishness.

Within half an hour all of the other students appeared. Even his own Fan girl, Hinata Hyuuga. The girl had some serious issues caused by her clan. Her father more then the rest. She had no self esteem, confidence or sense of self. It was warped by her fathers abuse. Overall she was weak and a perfect example of his beliefs. If they would just change their fighting style she would be a lot stronger. She just needed a far firmer sensei then Kurenai...

Naruto's head snapped up. Oh that was perfect. Redirecting his gaze to the girl he penetrated her mind with a surprisingly great amount of difficulty and planted several suggestions. If it worked, and it would, She would seek out the Help of Anko Mitarashi for Taijutsu, Weaponry and Jutsu training. It would also give them both a much needed close figure and boost Hinata's confidence. As well as to He may not have been a kind man but he did feel a limited Kinship with Anko and Hinata. They had both been pariahs and survived, well kind off in Hinata's case. But to thrive they would need a push in the right direction.

He also placed a few thoughts for her to consider her dream as a medic Nin.

Smirking Naruto was very pleased. He just made a possible powerful enemy. He did not care, it was better then crushing ants. This way he had a strong opponent. Also it would send a message that The clans are idiots. It was perfect really.

Then he heard a rather familiar noise, and shook his head. It was the Sound of two rabid fangirls who would kill anything or one to sit next to the object of their obsession. In other words it was Sakura Haruno and Ino Yamanaka stampeding to the academy to have the honor of sitting next to their precious Sasuke. It was times like this that he was glad that no one knew of his Heritage as it gave him the freedom of privacy. Or at least it gave him the opportunity to ditch his guard and train. Same thing really.

After a Sakura and Ino embarrassing every Kunoichi in existence, Iruka came into the room. He assigned the teams, gave a Speech then left. Only Naruto and Shino noticed his wounds. But Naruto knew what had caused them. Mizuki had attempted to steal the Scroll of Seals, which only has one seal on it. While Iruka and Mizuki fought Naruto read the scroll and copied it with his Sharringan. No one suspected a thing.

(Teams are Canon)

After three hours, in which Naruto had left a clone, Kakashi finally began to arrive. Naruto had to roll his eyes, Kakashi was a prime example of why he hated this village. If the man put forth any effort he could become extremely powerful. Instead he is a High A rank ninja that is a tad powerful. It was sad really.

As the man came in he saw Sakura panting like a dog in heat over Sasuke. But he could not find Naruto.

" Where is your other teammate?"

Sakura seeing a chance to insult Naruto jumped up and screamed " We don't know that loser never came to class. Probably failed or ran away as no one wants him around."

Kakashi was a little annoyed, Sasuke was actually pissed, but Naruto, he was amused " Actually Haruno I am Here"

They all turned to find him but could not see him. " Where are you Naruto" Kakashi asked. The boy was a master at stealth after all.

"Here" They saw the wall ripple and then Naruto was there. Sakura blushed and Kakashi had to ahold a blush from appearing. The kid was the most beautiful thing he had ever seen. He was not into kids but he was not blind either.

Shaking his head Kakashi said " Meet me on the roof"

Both he and Naruto poofed and were gone. Sakura and The Uchiha Gaped at this. One Jealous and the other was Pissed. They both stomped up to the roof.

As they got on to the roof they were shocked to see Naruto already there. Sakura began to scream at him " How the hell are you up here and how did you hide in the classroom?"

Naruto looked at her and said " Well Haruno it was called a Genjutsu and Shushin."

Kakashi got them to settle down and began his introduction, After Sakura could not understand what they were supposed to say. Really, and she is the Top Kunoichi.

" I am Kakahsi Hatake. I have some dislike and ... and some likes as well. I Have no hobbies and as for dreams, Well you are not old enough for that."

Sasuku scoffed. Sakura Gaped and Naruto rolled his eyes.

"Okay Pinky your up"

Scowling at her name, Sakura went " I am Sakura Haruno, age twelve. I like, well the person I like is- SQUEAL" Naruto was very glad for his ear plugs.

After shaking his head to get the Hearing back " Dislikes?"

"NARUTO AND INO-PIG!" Everyone, even Naruto, had to shake their heads at her behavior. " My hobby and dreams are..." She began to cackle while looking at Sasuke.

Naruto seeing Kakashi's confusion " She likes to plan how to rape him or get pieces of his flesh to cover her Sasuke Shrine with. Then she wished to marry him, become his wife and Rule as Miss Uchiha."
Sasuke Blanched, Sakura turned red and Kakahsi giggled.

"Okay Mr. Broods-a-lot. Your next"

Scowling Sasuke gave his normal bullshit about killing Itachi and Restoring his clan. Naruto scoffed. Itachi was already in ANBU at this age. Sasuke was pathetic compared to him.

Without prompting Naruto went " I am Naruto Uzumaki. I like to train, read, learn, and create. I dislike arrogance, fangirls, those who ride on their names, lack of progress, hypocrites, Those who judge without understanding and more. I loathe this village and all of its inhabitants Save Kabuto Yakushi. I also loathe all of the Hokages and the clan's traditions. My Hobbies are the same as my likes. My dream is to know as much as I can and put it to use."

Kakashi had to Narrow his eyes. It would seem that Naruto Knew of his burden and his heritage. This was not good, the boy may desert the village.

After Telling His students about the Test and not to eat breakfast, he left to go talk to the Hokage. This could be quite urgents.