This is just an encouragement to the disillusioned men and women out there that take issue with some of what orthodox Christianity purports. I, too, have a difficult time with some of the passages in the Bible that talk about worldwide floods and men staying alive in the belly of a huge fish for three days before being vomited back onto dry land. I don't understand completely why God allowed... no, encouraged the decimation of the Canaanites in Joshua. And going back to that flood thing, I still don't see how there could have been enough room on that ark for two of every kind of animal on the face of the earth, PLUS enough room for food for all of those animals, and still have the ark float, and still have enough living room for Noah and his whole family. I mean... ask a zookeeper how much food an elephant can eat in a week, much the less 40 days! And how about the crocodiles? What did they eat? Anyway, I'm getting off topic.
I am familiar with doubt, but I believe it is a necessary companion for anyone who seeks true faith, which is as rare as it is pure. Jesus died to take away our sins - not to take away our brains. I think this kind of intellectual (or common sense) approach to some of the blunt, right-in-front-of-your-nose kinds of questions is not antithetical to faith, but on the contrary is necessary for its refinement.
Maybe you're still wandering about in the thick forests of cosmological ambiguity, but as J.R.R. Tolkien once said, "Not all who wander are lost."
Take courage; persevere. We may not see clearly yet, but all will be revealed in time. In the meantime, consider it pure joy when you wrestle through some of the issues, because you know that if you persevere, you will be a changed person on the other side of it. And maybe then, we can all learn something about God from your experience.