I think Naruto and Daredevil are the obvious main focuses. But also, Elektra from Daredevil's world could be a great addition. She could have some sort of connection to a female ninja in the Naruto universe, like Sakura. Sakura could learn a thing or two from Elektra's combat style, and Elektra could be intrigued by Sakura's medical ninjutsu. And then there's also Itachi. His complex backstory and powerful abilities would make for a great interaction with Daredevil, especially considering Daredevil's sense of morality and Itachi's own moral dilemmas.
For me, Naruto and Daredevil are the core characters to focus on. However, we can't forget about characters like Rock Lee. His dedication to training and his unique fighting style could be contrasted with Daredevil's own martial arts skills. Also, Matt Murdock's (Daredevil) relationship with Foggy Nelson could be explored in the context of the Naruto universe. Maybe Foggy gets some sort of ninja - like power too, and they all have to work together. And of course, Gaara would be an interesting character to bring into the mix. His dark past and his control over sand could be a great counterpoint to Daredevil's acrobatic and sensory - based fighting style.