I don't know if Orochimaru would help Danzo in this without an ace in his sleeve. He's too sly for that. Hopefully Danzo's tale ends here. He's too stupid to live long in this world. If he turns out to be an actual headache it will be so annoying. How do you try to make someone into a God without a failsafe in case you succeed? I would've had the whole mountain rigged to blow and the bone clone on standby to dissolve Danzo at a moment's notice.

Also for Bingo Book name... How about relating it to his combat abilities? Minato was the yellow flash for his speed, Sakumo Hatake was the white fang for his sword. If the MC specialises in fuinjutsu, the Red Letter may be a funny play on words. MC is Chomei's jinchuriki, if he gets some sort of armour from Chomei Chakra Mode, then something like the Crimson Knight? You might put him in the Bingo Book already since he is the genius who saved saved Uzushiogakure from destruction while dealing significant damage to like 4 villages, then immediately reinforced his village by recruiting a clan that can contend with the Uchiha. In that case, something like the Scarlet Sage could work, though its ambitious for a what, 5 year old?

The academy shouldn't only be teaching basic maths and how to throw shuriken. You hyped it up that it would tailor itself to its students to create capable shinobi. Survival in the wild, politics of the ninja villages, as well as chakra beasts taming and summoning are all things the MC would have little understanding of currently. I don't mean chakra beasts like the Toad sages, but more like Kakashi's ninken. Besides the taught content we still need characters to interact with. Friends his age that make us readers actually care for the village. The academy is an excellent place to introduce not only friends, but also rivals. Skipping over this will make the village just unimportant background that the MC is protecting just because he can. Speaking of the village, give it some distinct features. Konoha has its Hokage wall, Kumo is on mountain peaks, Suna looks like a giant colloseum. What does our village look like? As for the Female Lead. It may be early to actually introduce the end game one. I'd say to have him on friendly terms with a Chinoike girl for now. In fact, make it so that she doesn't actually like him, but is forced to cater to him because he saved her family. This will make her far more interesting than some rescued damsel since the MC can sense her actual feelings even when she "confesses" to him. She can grow to like him because he's reliable, but also chastise him for arrogance or recklessness.

This is pretty good so far! Can't wait to get some consistent side characters, as well as a bijuu. This fanfic has such good potential. I'm pretty tired of the the "respawn in Konoha, hide talent from Danzo" routine, so finally having something that moves away from that is a breath of fresh air. Also, please don't make the rest of the villages a bunch of buffoons. When fuinjutsu is involved in Naruto fanfics, things get crazy quickly. Instead make them threats, political or otherwise. Danzo's Root is famous for instigating conflicts between foreign villages, perhaps Konoha uses them to make a village attack the land of whirlpools. Or perhaps they send a diplomat, maybe Tsunade, to bribe and garner influence with the elders, creating a Konoha faction in the village. Maybe Konoha starts covertly attacking shipments of seals, making it seem like we're against the village missing the shipments. Konoha says that it's bandit attacks and they offer to help in exchange for lower prices, making them seem favouratised to the other villages again. Consider geography and trade routes, as well as the farmland needed to maintain a village of 10000 people. Have diplomats, ambassadors, maybe even kids from other villages in the academy. Kagura's eye is a bit overpowered, so have fun with it. Until the main character is strong enough to protect the village from all threats keep dabbling in the politics. Also, don't be afraid to completely shift the plot. Maybe in the hope of getting their hands on the MC, Konoha kills Kushina under "mysterious circumstances", now requiring a new jinchuuriki for the 9 tails, not knowing the MC is already occupied. Maybe without access to the remains of the Uzumaki, Minato is unable to enhance the flying thunder god seal, meaning Konoha takes severe loses on the Iwa front, or Minato even dies to Kumo. Finally, take the Uzumaki in more directions. Having them just make a seal for any problem they encounter is boring. Exlore medical ninjutsu, summonings, senjutsu. Don't abandon the seals by any means, but use them more as boosters than fully fledged solutions. Enchant weapons, use Tsunade's Strength of 100. I think summons and a taijutsu style is already in the works so keep going!