One of the challenges could be uniting the people of Whirlpool. They may have different ideas and loyalties. Fem Naruto would need to gain their trust and respect. Additionally, resources could be scarce, and she has to figure out how to manage and allocate them effectively to build a strong Whirlpool.
He might face challenges like maintaining order among the chaotic and often unruly denizens of hell. There could be powerful demons who don't want to follow his leadership, and he has to use his skills and wits to subdue them.
Maybe through her exceptional ninja skills. If she shows great power and strategic thinking, the people of Whirlpool might choose her as their leader.
One challenge could be getting the Saints to adapt to his unorthodox methods. Since he comes from a different world with different fighting styles, the Saints might find it hard to follow his lead at first.
One major challenge would be trust. In the underworld, everyone is out for themselves. Naruto, with his trusting nature, would find it hard to know who to rely on. Another challenge would be maintaining his moral compass. The underworld is full of immoral activities, and he'd have to find a way to not get completely corrupted. Also, he'd face constant threats from rival underworld groups who would see him as a threat to their power.
One big challenge would be winning over the trust of the existing Akatsuki members. They have been following a very different ideology, and Naruto's more positive and peace - loving approach would be quite different for them. Also, the ninja world would be very suspicious of Naruto leading such a feared group. He'd have to prove that his leadership is going to change the Akatsuki for the better.
Naruto would face a great deal of challenges. Firstly, the Akatsuki members are used to a certain way of doing things. Changing their mindset would be tough. Secondly, the other ninja villages would be very suspicious of Naruto leading Akatsuki. They might see it as a threat rather than a positive change. Also, Naruto would have to deal with the internal power struggles that might arise within Akatsuki as some members might not be happy with his leadership style which is more about friendship and peace compared to the previous leadership.
One challenge could be getting enough resources. Rebuilding an entire place like the Whirlpool requires a lot of materials, and they might struggle to find or afford them. Another is dealing with the opinions of other ninja villages. Some villages might not be supportive of the rebuilding for various reasons.
One major challenge would be changing the Akatsuki's reputation. They're known as a group of villains, and Naruto would have to work hard to make them seem more like a force for good. Another challenge would be dealing with the internal power struggles among the members. Some might not be happy with Naruto's leadership style. Also, he'd have to face the opposition from the Hidden Villages who would be very suspicious of his new role.
She might have trouble adapting to the past's way of life. The technology and social norms could be very different, making it hard for her to fit in.
The secrecy that surrounds Itachi's past and his actions could be a major challenge. Fem Naruto might find it difficult to fully trust Itachi when she discovers parts of his past that are morally ambiguous. Also, Itachi's loyalty to the village in his own way might conflict with Fem Naruto's more straightforward ideas of justice, creating friction in their relationship.