How did Naruto restore Kakashi's left eye?
It was thanks to Naruto's new power: Ying Yang Release that he was able to restore it. If you remember  Hagoromo Ōtsutsuki  transfer his powers to Naruto (and Sasuke). The answer comes from the Naruto Wikipedia:


   After receiving power from Hagoromo, Naruto Uzumaki gained the ability to use Yin–Yang Release to stabilise life forces and restore missing organs through physical contact. However, there appears to be a limit to the extent to what this power can heal: While he was able to save Might Guy from the normally fatal consequences of unleashing all Eight Gates, he was unable to repair the damage done to his leg as a result of using Might Guy, and Guy spent the remainder of his life wheelchair-bound. Naruto was also able to resuscitate Obito after the Ten-Tails was extracted from him, but both were aware that his death was unavoidable when he was struck by Kaguya Ōtsutsuki's All-Killing Ash Bones.