Naruto may face resistance from within the village or other shinobi countries. Some may not want the Uzumaki clan to regain its former power. Also, there could be a lack of knowledge about Uzumaki traditions. Naruto would have to search far and wide to find people who can teach the new Uzumaki members about their heritage, which is a big challenge.
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.
Naruto is likely to be the catalyst. He has the influence and the will to bring together the scattered Uzumaki members.
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 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.
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 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.
Well, he could start a family with Hinata and have lots of kids, passing on his Uzumaki bloodline. Then, he could encourage his friends who have some Uzumaki connection, like Karin, to also have families and pass on their Uzumaki genes. He could also set up a school or training center in the Uzumaki land, teaching the Uzumaki ways of life and ninjutsu, which would attract orphans or those who want to be part of the Uzumaki clan.
In the fanfiction, Kakashi might face the challenge of Naruto's insecurities. Naruto has always had a complex about being alone and not having a family. Kakashi would have to find ways to make Naruto feel secure and loved. Also, dealing with Naruto's powerful and sometimes uncontrollable chakra could be a problem. Kakashi would need to train Naruto to master his chakra properly without it overwhelming him.
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 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.
Well, first of all, Naruto would need to address the stigma and fear that might be associated with the Uzumaki name due to past events. He'd use his own story of being an outcast turned hero to inspire those with Uzumaki blood. He could also establish a safe haven for the Uzumaki clan, a place where they can live without fear of persecution. And of course, he'd train the new Uzumaki members in combat and survival skills, just like how the Uzumaki were known for their strength in the past.