Well, Naruto being sealed away would face many difficulties. Firstly, he'd lose the opportunity to train and grow stronger with his friends. Secondly, he might struggle with self-doubt and fear of being forgotten. And lastly, there'd be the constant battle to keep his hope alive in that sealed state.
He faces many challenges like dealing with hostile forces trying to stop him and finding resources to build the village.
He faces tougher opponents. In the Chunin Exams, the competitors are more skilled. Naruto has to deal with more complex jutsus and battle strategies from his rivals. Also, he has to prove his leadership skills, which is crucial for a Chunin.
He'll likely face physical weakness and the fear of not finding a suitable donor in time.
I'm not entirely sure as I haven't read that specific fanfic. But it might be about Naruto being sealed away in some way, perhaps in a different scenario from the original story. Maybe some new villain or power manages to seal him.
One challenge Naruto might face is Sasuke's own will. Sasuke may be so consumed by his thirst for revenge or his dark path that he doesn't want to be brought back. Naruto has to break through that mental barrier. Another challenge could be the external forces that are influencing Sasuke, like the people or organizations that have turned him to the dark side. Naruto has to deal with them as well.
One major challenge would be survival. Outside the village, he no longer has the support system of the Hidden Leaf. He'd have to find food, shelter, and deal with potential attacks from other shinobi or bandits. For example, in the wild, he might struggle to find clean water and safe places to sleep.
One challenge could be acceptance. Naruto has always been known as a boy in the village, and suddenly becoming a girl might make some people distrust or be suspicious of him. Another challenge is physical. His fighting style might need to be adjusted as his body is now different. Also, he might face different social expectations that he's not used to.
You could try searching on fanfic websites like FanFiction.net or Archive of Our Own. Just type in 'naruto sealed away' in their search bars and see if it comes up.
One possible reason could be that his godlike powers were seen as a threat. The village elders or some powerful forces might have feared that Naruto, with his immense strength, could lose control and cause destruction. So, they decided to seal him away to protect the village and the world at large.
One challenge would be living up to Itachi's expectations. Itachi is a prodigy, and Naruto would have to work hard to match his skills. Another challenge could be dealing with Itachi's secretive nature. Naruto is used to open communication in his team with Kakashi and the others, but Itachi might not be as forthcoming. Also, Naruto might face opposition from other ninja who don't trust Itachi, and being on his team could put Naruto in a difficult position.