Do you really need some bibliography listed here? How about you take good math foundations, then learn about scientific method, then learn about quantum theory, then see how physical chemistry and atom theory follows from quantum theory, then go to organic chemistry, chemical bond theory, then learn about biology, cell theory, genetic and molecular biology, evolution, learn about diversity of life, astrobiology.
Yes, I've done that (well most of it - I hold Master of Sciences degree from Cambridge University). And yet I also believe the claims that the Bible makes about itself, about God, and about us. I believe that the historical authenticity of the text stands up to rational scrutiny. And I don't see any of the things you've mentioned as being contradictory to it. Exactly which religion is disproved by tectonic plate theory?
It is important here to distinguish between the core beliefs of the religion (and I'm going to speak specifically of Christianity, i.e. what the Bible says) versus the traditions, practices and interpretations of strictly human origin (dogma as you put it). Somebody else mentioned Galileo. Yes, he came into conflict with the church authorities when he showed that Earth was not at the centre of the solar system; but it wasn't a "disproof of religion" as the Bible doesn't make that claim. The suggestion that it did came partly from tradition of the prevailing mindset, and partly from an excessively literal reading of verses in Psalms or Ecclesiastes which say things like "the sun rises". (How can I say that one interpretation is excessively literal? Psalms is a songbook. The Bible is a collection of about six different types of literature, and you can identify the bits which are narrative and can be taken pretty much at literal face value, and the bits which are poetry and a more metaphorical approach is justified. When it says "the sun rises" in Psalms that's no more intended to be a definitive statement of relative motion, than when Rolf Harris sang it).
Not to say that all dogma is wrong - to fully understand the Bible would be more than a life's work, so I'm glad that people have given me a useful shortcut by summarising the flow of it. But I don't accept their words blindly - I check it for self-consistency, for consistency with the primary source (the Bible), and for consistency with my experience and understanding of the way the universe works - including my scientific training.
You claim "religion [...] makes a virtue out of accepting dogma" (and maybe some religions do - it's difficult to argue against such generalities) but mine doesn't, and I certainly don't think that's a biblical principle. On the contrary, there are number of biblical examples where people, on hearing something from their religious leaders, are commended for taking a sceptical (dare I say, evidence-based reasoning) approach by checking up on it first to see if it's true. (Acts 17:11 is the first one that comes to mind)
And then there is belief in something based on no evidence. You could say, it is based on ignorance. This kind of belief is called faith.
No, I don't agree that those terms are equivalent. Faithful Christians are no more ignorant for believing in God, than an atheist is for not doing so.
Sorry for not responding to every point in your post, but I have a feeling that I'd be here all day if I tried. Can I suggest if you're genuinely interested in how I might justify my disagreement with your points of view, that rather than try to continue a long thread in here, could I point you to a video of an Authors@Google talk by Tim Keller (author of "The Reason for God") in which he expresses similar ideas much better than I can.
Incidentally, I'm not typing this with any particular aim or expectation of trying to convince you that the Bible is true. I'm just arguing that believing it is at least rational, and compatible with a scientific approach. If there were credible contradictory evidence then faith would be preposterous, but I am convinced this is not the case.