Well, I'd like to go through every page and answer questions but I'm so far behind that I'll just speak very generally on some of my thoughts for now:
Science is great, but I think it's disingenuous to totally discount God because of perception. I'm not interested in getting into a pissing contest of who can be more prideful and superior. In science, evidence means nothing if it is misinterpreted. So we are presented the same facts, the difference is interpretation.
If God created the universe, then he would be revealed in everything. That is what I see. People care about the immaterial things, they have needs to create and for it to be functional as well as aesthetically pleasing just as the universe is and many things in it. I see good versus evil manifest itself everywhere from media, entertainment, to the world, to your own personal battles. Before people saw atoms and cells, they were unseen. Didn't mean they did not exist. Just like laws of nature and math formulas. They are discovered, not invented. I believe that is another way of God revealing himself through nature and science. You need the right lens to see God. He has to be revealed through the natural if he created it, but you won't see his nature through the natural mind just as you won't see atoms with the natural eye. I won't quote Bible verses because I know people don't like it and it does nothing for them, but that is where being led by the Spirit comes in. Now, I'm sure there are people that have found ways to refute everything I just said, but that is what I mean by interpretation and I'm trying to explain it in the most practical way for you. Regardless of interpretation, I believe there are concrete right answers, even if many sides get it wrong.
I don't believe this for my own self because it makes me feel warm and fuzzy and helps me. It's not a mind game. Spare me that, I can easily go without the ridicule and people assuming you are an idiot based on nothing but the fact that you believe in God. But you can't get around believing. So when many atheists ask for evidence, what they really want is an out so they don't have to believe (or it's a trap question).
But ask yourself this question, what would it take for you to believe? I saw an atheist say if two moons appeared out of the sky. I doubt that would work. He would try to find scientific explanation, and if he couldn't, people would find a theory that they would accept. If you said I need God to appear in front of me right now, I'm sure you would find what you perceive as a rational explanation like it's a hallucination or something. I'm not saying everything unexplained equals there is a God, but I'm trying to show you your own mind. Science tries to rationalize the irrational many times. Understand that I'm not trying to criticize, but get you to think that you may not be seeking even an earnest discussion if you come to the conclusion a natural or supernatural evidence means nothing to you in the end.