I know but the bigger issue I have is assuming that base form naruto about 6 months in the future is both stronger and tougher than his cloaked version from before then to a degree that scaling between the two is unreliable. While that is a good amount of time, seeing as the arc is all about how Naruto can't make time for his family and the lack of real threats that'd he'd be preparing for as hokage, such a drastic increase in strength and durability that his base form exceeds his cloaked form feels unsubstantiated.
I understand your thinking but see we have problems similar to these, In Sakura's novel, she fights with Kido, who was just a random ninja who used a drug that gave him a copy of kurama's power, but in a much smaller scale than Naruto's, and not even the KM he had, and she fought him equal to equal, she hurt him a lot but she was also extremely hurt, With this drug, these characters were stated to be orders of magnitude stronger than their base form, however, their base form had a level similar to Sai and Ino, i.e. tier 7, even with the multiplier it must not exceed tier 6C, which means that Sakura in that phase was in that same tier. After that she leaves to travel with Sasuke, and becomes pregnant, after that she no longer enters battles and becomes the director of the hospital, that is, there were no battles or training for her to level up to tier 5, nor did she receive power from any god, so it doesn't make sense for her to be tier 5.
Shin problem is even bigger, he's just another one of Orochimaru's artificial humans created with the DNA of some random uchiha, after being created he went crazy for Itachi, and then planned to kill Sasuke. There isn't a big time gap for him to reach the tier 5 suddenly, orochimaru isn't able to create an artificial human that has tier 5, Amado needed the DNA of a God for this, that is, this makes everything very imprecise. You said that you don't think a huge increase for Naruto in 6 months is plausible, however the raise for Shin and Sakura is even less believable.
Shin shouldn't be tier 5, in addition to the various implications already left in the post, all of his supposed deeds can be justified.
•Shin hurt Naruto:
His power does not increase the AP of the tools he controls, this was never mentioned anywhere he just controls them telekinetically, so the fact that he hurt Naruto could just be an outlier, because Naruto was able to resist piercing attacks other times. If the outlier option isn't to the liking of some, we might just scale his hax to tier 5, as it currently is, but we must remove the tier 5 defense.
•Shin resists Sasuke's fireball:
This part is simple, as I mentioned in another comment, this version of Sasuke was EXTREMELY NERFED, He lost rinnegan tomoes, it's the weakest version of him in the new age, weaker than the version of the Urashiki arc, which was completely humiliated, It has been implied several times that the lack of chakra can make Sasuke very weak, and we know that the AP of a Naruto character completely depends on the amount of chakra he has in his body, this means that the strength of the fireball might have been way below tier 5.
Naruto, Sasuke and Madara had to go through several evolutions, several upgrades and even so, and aside from the fact that they are the reincarnation of an Ootsutsuki, still had to receive huge amounts of external power (Juubi/Shinju and Hagoromo), and that's the only way they managed to reach that level. I think the best solution here is to find a solid rating for Sakura, based on the fight with Kido (in her novel), and scale Shin for her, he would scale to her in physical, Speed and Defense, and would scale to tier 5 via hax.
