Jonathan, I hear your worries on some points. Yes, different stories have different focus. Likewise, we can focus on one thing or another. I tend to read randomly or to read things I am interested in. It is not a perfect way, but it opens me to scripture. I also read things that others comment on or quote and go and read more of those passages associated with those. Little by little doing this I began to sort out, without trying to, previous issues with scripture. For example, I for one can take or leave Corintians (parts of) because they feel more like a human priest telling the flock to follow a bunch of human rules. But that is what they needed to hear no doubt, although I find the writing style to be sort of different (for me) than other parts that seem better written.. But there must be a reason for that, the question of the audience and focus. And sometimes we too need to hear things in a direct way too. Once I accepted Jesus, my heart was at rest, I was not feeling it as a point of contention but just assumed I would grow to understand any parts of scripture that for now feel alien to me. It used to bother me too, that the OT God seemed violent and punished man. After all, man is finite weak has the deck stacked against him and also on top of that the evil ones plague him. But none of that bothers me now. For one, man is not being asked to do impossible things. He is only being asked to accept and love Jesus. How hard can it be to love Jesus, a beautiful, perfect being who loves us back. The impossible things we deal with are that the human race was punished, fell from Grace because Eve listened to Satan. It seems unfair that because one human, our human parent, chose to disobey that we are all punished. But keep in mind that when Eve disobeyed she was not the finite creatures we are. She was a being who would never age, who had communion with God in the Garden, whose needs were all met in spades. The only rule was don't eat that. In eating it she disobeyed the Lord and risked displeasing her husband too. A cynical argument I have heard often is that well, God knew they'd sin so therefore he set them up, that in the same way we are set up now since the Lord knows who will accept Jesus and in advance has pre-sifted man. Those he rejects and destroys then had no way to escape that fate.
It is very hard to answer this question Jonathan because we have to make assumptions about who God is and what he pre-ordains and what he allows for us to actually do, i.e., is there really free will. The best human minds in history can't answer if there is free will, so how could I. My answer is that in humility I must accept I don't know everything. I have a finite view of reality and can't possibly second guess what God knows, does, thinks. My only task is to have FAITH in Jesus and to let the Holy Spirit in my heart to teach me. Yes, I have to go through life daily, feeling weak, feeling a lack of control, being unsure that I have a clear and certain picture of what God wants from me. Because I don't know much it forces humility. I have to hold my silence a bit more often with others, wait, cease to judge for myself. I feel peace and joy to have accepted Jesus but that doesn't mean that I know everything now and that all of finite existence and the choices I make there are crystal clear or that I understand, with perfect x-ray vision every line of the bible.. I do think though that having more humility helps me avoid doing things that I would regret since I am less apt to think I have the answers and leap into things.It also lets me approach scripture with an open heart.