You know here is what I think should've happened when it came Part 2 and you would have to slightly tweak the ending of Part 1 for it to work..
A semi-change to Part 1's Ending:
Instead of Naruto losing to Sasuke at the end of Part 1, he defeats Sasuke and brings him back to the village. Sakura could still end up training under Tsunade after witnessing how far Naruto was willing to go to save Sasuke for her. Sakura witness's the beating that Naruto took from Sasuke and sort of regrets it because she believes that she was the cause of his injuries. Sasuke having learned his lesson values Naruto's life even greater and vows that next time he and Naruto fight it won't be so easy for him. Despite gaining self-respect for the people around him Sasuke vows that he still wants revenge for what Itachi did towards the Uchiha Clan. Learning from Jiraiya that the Akatsutsuki are after him, Naruto vows that he will stop all the Akatsutski members and that he will be stronger the next time he returns. Part 1 ends with Naruto leaving the village with Jiraiya as it did originally.
Here is how Part 2 could work with the Part 1 ending I'm suggesting (Not I don't have the entirety of Part 2 figured out):
Rescue Kazekage Arc:
Opens up the same way as the manga did with Naruto and Jiraiya returning alongside Sakura and Tsunade welcoming them for their return. Kakashi and Sasuke are training and the test to see their skill is for Naruto and Sakura to team up in a battle against Sasuke. Showcasing his abilities Naruto goes into the battle with Sage Mode against Sasuke surprising Sakura, Kakashi, and Tsunade (obviously not Jiraiya). Throwing off Sasuke, Sakura uses his "monster strength" with Naruto dodging the impact as they both defeat their teammate. Using Sage mode puts a toll on Naruto as he hasn't completely mastered it as of yet which Sakura compliments Naruto of how she found it impressive.
Sasuke at the very least would've learned Chidori stream and possibly Chidori light blade (with his sword) with the test fight, and the fight itself would be relatively the same as it was in Part 1. The rest of the arc continues to be the same with Deidara and Sasori capturing Gaara alongside Team Kakashi and Team Guy coming in to fulfill their duty. Naruto would still go into his one tail bursting two tails and of course Chiyo's speech to Sakura about choosing her jutsu to save somebody she deeply cares about rather than an old hag like her, and of course with her dying. Even though Naruto would be relieved with Gaara saving he would vow that the Akatsutski need to be stopped, and possibly sensing Tobi from the distance maybe like see his shadow before he disappears.
Sai and Sasuke Arc would be removed for obvious reasons in the context of this version of Part 2.
Hidan and Kakuzu arc could still work you just have Team 7 training together while the events still playout the same way as they before. Only you have Sakura unlock the Byakugou seal here, Naruto gaining his wind nature and possibly learning another jutsu like the flying thunder god (not master just learn it), and Sasuke could possibly learn about Hawk summoning during the training. Everything ends once again you see Tobi watching from the distance of the battle as he notes Kakashi still hasn't changed that much, and how he's gonna try harder to capture Naruto Uzumaki and has some interest regarding Sasuke Uchiha.
Persuit of Itachi I see is the arc where Orochimaru comes back into play because Tobi not only wants Naruto captured, but he has personal buisness with Sasuke. Both of these character have on common goal getting Sasuke, and knowing that Itachi is on the move to capture Naruto, Kakashi decides to split the team with Sasuke and Kakashi dealing with Itachi while Naruto and Sakura deal with Orochimaru.
Ironically here is how the battle would playout for Naruto and Sakura vs Orochimaru, the setting would be at the Heaven and Earth Bridge. Orochimaru taunts Naruto about how useless he is compared to Sasuke which makes his blood boil getting him to the point of hitting four tails after attempting to catch him off guard by attempting to kill Sakura. Since this would cause Naruto to hit Four tails, we have a similar scene with Sakura trying to stop Naruto and ultimately succeeds with them seemingly defeating Orochimaru. Sakura ultimately recalls something Tsunade taught her about a jinchuriki when they become the monster and recall what Lady Chiyo said using the jutsu (Yamato would've used) to revert Naruto to what he was before he went insane against Orochimaru.
For the Sasuke and Kakashi vs Itachi fight lets just say that Kakashi does whatever it takes against Itachi before he falls under the same jutsu Itachi put him under back in Part 1. That would ultimately lead to Sasuke and Itachi having their fight with the Susanoo and Orochimaru reappearing before getting stabbed by the Totska Blade. Itachi dies by the hands of Sasuke, who of course passes out from Exhaustion while Tobi shows up taking Sasuke and looking at the unconscious Kakashi stating how once again he couldn't protect anyone just like her.. (alluding to Rin) and then disappears.
Arc ends with Naruto waking up from his hospital bed with Sakura by his side looking concerned and Naruto giving his smart ass smile tells her it's nothing to worry to about before getting a slap from Sakura as well as a hug causing her to burst in tears leaving him confused. Sakura while crying tells Naruto to never go that far again for her sake which ultimately makes him smile. While doing so Naruto realizes that Sasuke isn't there and Sakura once again looks sadden about it before he tells him "Kakashi said told me that Sasuke disappeared after the fight against Itachi." Finally we have the same scene occur between Sasuke and Tobi about The revelation behind Itachi Uchiha and we have the arc conclude with Tobi telling Sasuke "Itachi swore to protect Konoha, and now that you know the truth what will you do, Sasuke?"
The reason why I would end it like that is because you wouldn't really know what path Sasuke would chose after hearing the truth.
Well that's as far as my ideas would go for Part 2 with a bit of tweaking from Part 1's ending.
Persona 5 hype 
