Well, he might have, but he would be cured soon enough, for better or worse...

Sorry but it seems that you misunderstood something, the nine-tails incident happened the night before our MC reincarnated.

A little clarification here - the soul energy would take 30 days to refill every time he time travels, I don't remember if it already explained at this point or not, so... sorry for a possibly a spoiler here

Yea I know, sorry for that, early chapters are something that I'm not proud of, it's my first writing work and there is also a language barrier so early chapters are not that great, but it's getting better in later chapters, that is for sure.

The idea was that those stuff was just a great boosts but not picking it will not limit our MC. For example, any shinobi can master any of the five basic elements regardless of their affinity, it's just would take a lot of time and efforts.

Nope, I don't think there would be anything shinobi related for unauthorized civilians at all, at least not in my story. You see, I make it somewhat hardcore. In many fanfics there is a jutsus in the academy library for free, but in my story there isn't any, and jutsu are heavily guarded and stuff like that.

Well, the idea was that the difference between the normal people chakra amount and the academy student that worked on it for a year, would be very big. In numbers it will be: normal human - 5 chakra, second year student - 30, Genin - 100. The crazy growth come from that, but in the bigger picture perspective it's not that significant, like growing chakra from 5 to 20, like it's four times bigger, but it's still just 20. I hope that makes sense.

Just for some stuff for the future, there is a reason

Mieko being mentioned more and more recently. Maybe, just maybe, there some sort of her revival is coming? How about to force Nagato with spirit transformation jutsu to revive her instead of Konoha cannon fodder after Nagato came to Konoha to die? Why let Nagato to waste himself on reviving Konoha fodder and Kakashi when he can revive Mieko instead, right?

That is an interesting take on the matter, I like it. The problem is that Danzo is a member of the council, that means that he can't be easily dealt with, and root is the subdivision of ANBU, that is much higher in the power hierarchy than the police force.

That is obvious of course, but the problem is deeper, as they was preparing coup not without a reason, even without a coup they will be eliminated soon enough by one of the Danzo's schemes, at least in my understanding of the plot there.

Well, they definitely met, but are they friends already? There is a filler episode of shippuden where Itachi and Shisui were spend time together in the woods and fight a few root shinobi, Itachi was already using sharingan at that point and they become friends during that event, and considering that Itachi awoken his sharingan only a year after graduation during his teammate's death, I don't consider them friends yet. I hope that make sense

To answer the question of how MC's chakra grown so much with his spiritual energy alone - I'm going with the theory that chakra is the mix of physical and spiritual energies, but it's not 50/50 mix, it's whatever is there-mix, and until the disbalance not become too ridiculous, like 1to99 of value, there will be no other problems except the sage mode training problem, as it requires achieving the balance between 3 energies, physical energy included. And to address the Otsutsuki power - it's ridiculously strong and there is no point to consider it right now, as Elite Jonins are canon fodder for them and Kage level shinobi is just weaklings to them, so up to at least Kage level MC shouldn't even think about how to countering Otsutsuki. I hope that make sense. Also I'm glad that you notice MC's changing mentality, it's something that I planned a long time ago.

That might be true, but the idea behind that back then was that 1k points is the base, and abilities costs is based on the idea to limit what the MC can get in total, the abilities costs was not based on their actual value, I hope that makes sense

Sorry to hear that, I'm not read any story like that before but here MC has consequences and it's not entirely 'Save-Load'. He travels it time with his soul, so any damage to soul will be permanent. Later on he will probably travel in time with his whole body, so the same rules will be applied there as well.

In my understanding it's Might Guy is who has 0 talent in everything but taijutsu, for comparison. Yuta has decent talent, not very good but not bad either, to grow his chakra level to Jonin level in just 20 years in time-loops with his spiritual energy alone its something admirable, as most shinobi in the world are not able to get to the Jonin level in their whole life...

Yea, that's right, the arm will be back after traveling in time past the point in time when he lost it.

Yea, sorry about that, the early chapters are bad as it's my first work and English is my second language, but I'm trying to improve my writing in the process.

Time travel can be very confusing

Yes, he would have his arm back after he would travel back in time past the point he lost it, which he didn't done yet.