In harem fanfiction, Naruto could face the challenge of dealing with different cultural backgrounds of his partners. Since they come from various places, integrating their ideas and values into the new clan structure might be a headache. Moreover, resources are always an issue. Rebuilding a clan requires a lot of money, manpower, and materials. He has to figure out how to gather these resources while also maintaining his relationships in the harem. For example, some of his partners may have their own financial or family obligations that could either help or hinder his clan - rebuilding efforts.
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 challenge could be finding enough Uzumaki descendants. Since the clan has been through so much, there may be very few left. Another might be dealing with the political implications. Other clans might be jealous or fearful of a resurgent Uzumaki clan.
One challenge is the lack of pure - blood Uzumaki. Since he is the last one he knows of, finding suitable mates with enough Uzumaki blood could be difficult. Also, the Uzumaki clan has a lot of enemies. Those enemies might try to stop Naruto from reviving the clan so they don't become a threat again.
One challenge could be getting the other ninja clans to accept his new clan. The existing clans have their own traditions and power structures, and they might see Naruto's new clan as a threat.
One big challenge would be finding skilled ninjas to help him. Ushiogakure might not have a large population to start with. He'd need to either train new ninjas from scratch or convince others to join him. Another issue could be dealing with any existing rivalries or feuds in the area.
One challenge would be getting other shinobi to join. Some might be loyal to their existing clans. Also, there could be political opposition in Konoha. The elders might not be too keen on a new clan being formed.
In fanfiction, Naruto may face challenges related to politics. Other villages may see the restoration of the Uzumaki clan as a threat to the balance of power. They could try to interfere in Naruto's efforts through various means such as spreading false rumors about the Uzumaki or even sending spies or assassins. Additionally, Naruto has his own duties as Hokage, so he would need to balance his time between running the village and restoring his clan.
One challenge could be time management. Naruto is always so busy with his ninja duties, protecting the village and going on missions. Finding the time to sit down and write would be tough. Also, he might struggle with grammar and spelling since his ninja training didn't really focus on that.
One challenge could be gaining the trust of the Root members. Since Root has a history of being a secretive and somewhat feared organization, the members might be skeptical of Naruto's leadership. They're used to a more authoritarian style, and Naruto's more open and friendly approach could be met with resistance.
One challenge could be controlling the amount of natural energy he uses. If he uses too much, he might lose control and enter a berserk state like when he first tried to use Sage Mode. Another challenge is that his opponents might find ways to disrupt his connection to natural energy sources, leaving him weakened.