Some things just don't have a answer in this life. And the lack of a answer, don't automatically mean lack of God, it might just mean a lack of a answer and that is all.
Several things in the bible is more then just stories. For example Jonah in the belly of the whale is something that points forward to Jesus and the 3 days he were in the heart of the earth. We both know that it is impossible for a man to survive for days in the belly of a whale. We know that whales don't eat humans. And we know that if a human happened to be eaten by a whale, then it would be unlikely that the whale would spit up the human on the land. But as Christians we think that anything is possible for God, including to let a man be eaten and spitted out by a whale and for the earth to be filled with more water then there actually is on earth, like the story of Noah tells about. So things that seem impossible, can be explained by that nothing is impossible for God. Or we can think that many of the stories are symbolic in the way they describe things in a easy way, so that us humans can understand it, just like Jesus explained many things by using things that humans understand. Personally I know several things about the bible and God I just don't understand, and I've settled with this, that this is my lack of understanding, and not a lack of the existence of God, cause like you say: You know in your heart that God is real. If this was Santa Claus we believed in, then you would not know in your heart that he is real. But God we know is real, cause we hear the voice of the shepherd calling on us, and we follow the voice, cause we know that the shepherd loves us and are leading us to a good place.