One challenge could be getting the necessary resources. Uzushiogakure was destroyed long ago, so finding materials to build the village again would be tough. He might have to negotiate with other villages for supplies.
In many fanfictions, Naruto might use new jutsus or a deeper understanding of his own power. Maybe he taps into a more powerful form of the Nine - Tails' chakra and combines it with his Sage Mode in a unique way to overpower Pain.
In some fanfictions, Naruto's pain might manifest through his actions. For example, he could become withdrawn and isolate himself from his friends. This is because Naruto has always been a social person, so any deviation from his normal behavior could be a sign of his internal pain.
One possible cause could be his sense of failure. Naruto always wants to protect his friends and village, so if he fails in a mission or is unable to save someone, it can cause him great pain.
Well, Naruto might face environmental challenges. For example, if the toddler is in a swampy area or a place with a lot of quicksand. Naruto has to navigate through these difficult terrains while protecting the toddler. Also, if there are other threats around like poisonous plants or insects, he has to be aware of them too. He can't just focus on getting the toddler out, but also has to ensure their safety during the whole process. This requires his full attention and all his ninja knowledge.
His fighting style could become more aggressive. Without the fear of pain, he might be willing to use more extreme techniques that would otherwise be too dangerous because of the pain they cause to the user. He could push his body to the limit more often.
Konan could be really interesting. In some fanfictions, she might have a different backstory or motivation that affects the Naruto vs Pain fight. For example, she could be secretly trying to stop Pain from going too far in his destruction of the Leaf Village.
Jiraiya could be a great addition. Since he was Pain's teacher, his presence could add a lot of depth to the story. He could offer insights into Pain's past and also help Naruto understand Pain better.
One challenge could be the cultural differences. Naruto is from a ninja world, and the lycans have their own unique culture. Understanding and respecting those differences while still leading effectively can be tough.
He could feel it through a shared chakra link. Since they are related and Minato sealed the Nine - Tails in Naruto, there might be a latent connection that gets activated in the fanfiction, allowing him to sense Naruto's pain on a physical and emotional level.