Kawaki might resist Naruto's teachings at first. Since he has his own way of doing things, adapting to Naruto's values and training methods could be difficult. Also, the village might not fully accept Kawaki right away, and Naruto would have to fight for Kawaki to be accepted, which is a big challenge.
One challenge could be Naruto's stubbornness. Naruto has his own ideas and ways of doing things, and getting him to listen and follow Kakashi's guidance might be tough. Another is dealing with Naruto's past traumas. Kakashi would need to help Naruto overcome his feelings of loneliness and being an outcast. Also, Kakashi has his own responsibilities and missions, so finding time to be a proper adoptive father could be a struggle.
In this kind of fanfiction, Naruto might teach Kawaki about the values of the Hidden Leaf Village. Maybe he'd show Kawaki how to control his powers better. For example, Naruto could take Kawaki on training sessions similar to the ones he had with Jiraiya.
One challenge could be adapting to the team's dynamics. Team 8 has its own way of operating, and Naruto is used to his own style with his friends. For instance, they might be more methodical in their planning, while Naruto is more of a 'jump - in - and - figure - it - out' type. So, he'd have to learn to follow their lead sometimes.
He might face challenges like finding the right place to plant the tree. Konoha has a lot of regulations about what can be planted where. Also, he needs to make sure the tree gets enough water and sunlight. If it's a magical tree, he may not know exactly what it needs to grow well.
One challenge could be controlling the power of the Juubi. It's an incredibly powerful and chaotic force. Naruto would have to struggle to keep it in check so that it doesn't overwhelm him and cause him to lose control. If he loses control, he could end up harming his friends and allies instead of protecting them.
One challenge could be dealing with competitors. If his company is in a competitive field like ninja training, there might be other established companies or individuals who see him as a threat and try to undermine his business.
One challenge could be the cultural shock. Naruto is used to the ways of the ninja villages, and New York has a very different culture. Another challenge might be the language barrier. He would need to communicate with people in New York, and English might not be his strong suit. Also, the different fighting styles in New York compared to his ninja skills could pose a problem.
One challenge could be that the enemy is too powerful for Naruto to defeat on his own. He might have to quickly level up his skills or find allies to help him. For instance, he might need to convince some of the more reluctant ninja in the village to join him in the fight.
One challenge Naruto might face is dealing with the physical changes in the Kyuubi. Since it's a unique situation, he may not know how to properly support the Kyuubi during the pregnancy. Another challenge could be facing the judgment of the villagers. They may be afraid or not understand what's going on and turn against Naruto.
Well, for starters, Kakashi has to deal with Naruto's hyperactive and sometimes reckless behavior. Naruto often acts without thinking, which could put him in danger. Sasuke, with his complex emotions and the burden of his clan's massacre, is also a handful. Kakashi needs to make Sasuke understand that revenge is not the only way forward. Additionally, Kakashi has to ensure that both Naruto and Sasuke get along well with each other. There could be rivalry between them, and Kakashi has to manage that in a way that doesn't harm their relationship or their growth as ninjas.