I think “faith” as we would think of it here in the West is a very Abrahamic concept that doesn’t really have an equivalent in Japanese culture or religion. “God’s Plan for us all” isn’t really a thing in Shinto or Buddhism that I know of, neither really is your personal relationship with the Divine. Those deities are more massive aspects of nature who simply exist and don’t demand your love and surrender to their will. (Feel free to point out how I’m wrong, I’m not an expert in Eastern religions.)
So there aren’t that any manga or anime I can think of that are primary about a character’s internal struggle with belief in god or the gods. Even when they dip into Monotheist themes, like in Evangelion, it’s Shinji’s crisis of faith in himself not in a higher power. Shin Megami Tensei treats capital G God as a lunatic tyrant.
But if you want something, The Leftovers. Angels in America. Darron Aronofsky’s Noah. The Stephen King book Desperation. A Serious Man as mentioned before (or a lot of Coen Bros stuff, even Hail Caesar!)