Hi there. I'd like to assure you that asking questions is a good thing, there is nothing wrong with healthy skepticism. I think that as you study the bible and learn more about life and the universe, you will come to a greater harmony between all facets of knowledge. I've been a philosophical type since I was very young, always exploring and trying to learn new things. Since I became a Christian I've actually learned a lot and have in no way shied away from exploration. Like you I had many questions, and I still have questions, but the more I learn and rely on the guidance of the Holy Spirit, the more confident I am in the reliability of the bible as God's word. Now I'll try to tackle some of the specific issues you raise.
It is difficult for me to get behind something that on multiple occasions promotes mass murder, misogyny, and rape.
This is a loaded issue but I will try to sketch a summary of these objections. First, we must understand that we are dealing here with God, the very giver and sustainer of life. Yes, God kills people. The bible affirms that ALL human beings are fallen, evil, sinful creatures since the fall of man. Mankind has forsaken fellowship with God, the source of all good, and consequently we are by nature evil. So not only does God have the right to kill people, as the author of life, he is also just in doing so in light of the depravity of human nature.
Also keep in mind that God shows great patience in dealing with wicked people, giving them ample time to repent of their sins. Take for example the Cannanite nations the Israelites were commanded to drive out. These people had a habitual practice of rape, murder, incest, idolatry, even burning their children alive on alters before their "gods". This had been happening for a long time. The Israelites were enslaved in Egypt for 400 years, that's 400 years of time that God patiently gave these people to repent of their sins and turn to him; yet they only got worse. So God finally liberated the Israelites from slavery in Egypt and gave them the land these sinful nations had occupied, both as a promise to his elected people (the Israelites) and in judgement of the wickedness of the Canaanites. God commanded that these people be driven out, and they were. Any who remained were ordered to be slaughtered, so that Israel would not be corrupted by their evil practices. God is just in his judgements.
This is just one exposition of a small part of scripture, I suggest you undertake some serious biblical study of these areas you are having difficulty with. I will provide some links below to help you with this.
it seems that Christians are Christians because they were raised in a Christian culture
I was raised a lukewarm Catholic and became an atheist by the time I was nine years old. I was an atheist for a decade before I got saved. So my upbringing really had nothing to do with it, I became a Christian after having a powerful personal encounter with God. There are many, many testimonies out there of people coming to God who had no religious background at all. The very people you would least expect to be Christian, in many cases, get saved. There is a real supernatural power behind Christianity, Christianity is not really a religion, it is a body of truths revealed by the spirit of the Living God.
At this point I almost feel as though God is the reason I am an atheist
I greatly appreciate that you have been seeking God, I do, that shows that you are on the right track. However God is not the cause for your atheism. Our minds are corrupted by the power of sin, and in our natural state we are blinded to the evident truth of God. But God reveals himself in the very universe he created, the universe you take for granted.
The bible itself explains that scripture is foolishness to those who do not believe, because it contains truth that is spiritually discerned. Apart from the spirit of God its hard to make sense of. But the fact that you are seeking tells me that God IS in fact starting to move within you. I think your biggest hurdle to overcome is this false idea that the bible contradicts scientific knowledge and experience. There is a great deal of wonderful work that has been done revealing the consistency and compatibility of science and scripture. On top of this, there is a great deal of evidence showing the inspiration of the bible, such as fulfilled prophecy and the consistency of various types and idioms across the scope of scripture.
I'm gonna give you some links to some very helpful resources that should illuminate the intellectual viability of the historic Christian faith for you. I urge you to read through these resources diligently. Nothing is more important that your eternal destiny friend, so if the intellectual element is your biggest stumbling block, I want to make sure that you can get over that.
Also I highly recommend that you devote some time to bible study. If you are interested in delving into some in depth bible study, it will answer many of your questions and provide some stunning evidence for the inspiration of scripture. I would be happy to give some links to some exceptional bible studies on any and every book of the bible, just send me a PM, I'd love to help.
Here are some links I think you will find exceptionally helpful.
Defending Biblical Christianity | Reasonable Faith
Reasons To Believe : Where Science & Faith Converge
Evidence for God from Science
The Veritas Forum
Bible Questions Answered
After exploring all of this information, if you can agree that Christianity is an intellectually tenable position, I encourage you to explore the gospel of Jesus Christ. There is no more important message you will ever hear, your eternal destiny hangs on your response to it. Below is a particularly good exposition of the Gospel, I pray you will listen to it and I pray that God may move in your heart and convict you of your sin and your need of Christ. Repent and believe the gospel, and you will live.
Paul Washer, The Gospel. The most terrifying truth of Scripture... - YouTube
If you have any questions, or if you would just like to talk, I encourage you to PM me. I'd love nothing more than to talk with you one on one about these issues. Don't give up on seeking God, he is real, he is out there, he is not too far, and you WILL find him. I've been in your shoes and now I KNOW that he is real. Hit me up friend, I'd love to talk with you.