Starting off

I am a scientist at heart, which means I like structure and working with a method. I will tell your about the books I have read and what struck me when reading the Bible as well as anything I learned from attending services and from discussions with others. But this post is about the starting point; what do I believe in right now, what are my main questions about Christianity, what do I struggle with and so on.
What I know: I know there is a God. I have never doubted the existence of a higher entity, who was the beginning and who now watches the universe. This entity is all powerful and encompasses everything. I know Jesus existed; I remember reading a Roman document about His crucification in RE at one point but I never doubted that He existed, simply because of the impact His life and teachings had on the world. I agree with His teachings. He was inspired. They make sense. They are so simple and yet apply to everything: Love and honour God. Love your neighbour as you love yourself. (I'm paraphrasing. He said it nicer.) Can it get any simpler? It's brilliant. Also, I believe that he died for His beliefs and because of narrow-minded, power-hungry people. I have felt the Holy Spirit at certain times in my life but only when I was ready for it.
What I struggle with: God created the universe, yes, but who is to say, he actually cares about us like a father? Does he really listen to my prayers, when I am so unimportant in the big picture? Sometimes I can feel His love and I know that God is great and I cannot understand the extend of His love. But there are times when I doubt, when I know that I am no more important than anyone else.
Was Jesus really God's son? He most certainly was inspired by God but actually His son, that I find difficult to believe. It goes with the question whether God loves us personally; if he does, I can believe that He sent His son to die for us, but if he is distant, he probably didn't. Did Jesus really die and come back to life? Over the years I have meandered through different ideas about how it might have come about; all to avoid the big challenge of accepting the amazing miracle if he really was raised from the dead. There is something within me that does not want to believe it because it is just so irrational. So, definitely something I need to work on.
Does the Bible tell the literal truth? Let me tell you from the start that I know evolution to be a fact and that I am in no doubt about it. I read Genesis more as a poem about God's greatness explained to someone living a few thousand years ago. If I accept that though, what else is open to interpretation? Is the big flood a fact or a metaphor? Did Moses really divide the sea? Did Jesus really heal people by laying his hand on them? I will need to work through the bible and make sense of all the miraculous events described in it. As a scientist I know that will take it with a pinch of salt but does that make me less of a Christian? I need to find out.
What are your thoughts on this?