Utilizing each of the historical facts conceded by virtually all contemporary scholars, please produce a comprehensive natural explanation of Jesus’ resurrection that makes better sense than the event itself.
Well here are four that spring immediately to mind, and I'm confident I could think up at least a dozen more. The witnesses lied. The resurrection was faked by someone. The event was entirely made up after the fact by the authors of the gospels. Jesus wasn't really dead. Each of these explanations make much more sense than a guy coming back from the dead after three days, which is something that we all know is physically impossible.
Given the commonly recognized and scientifically supported belief that the universe (all matter, energy, space, time) began to exist a finite time ago and that the universe is remarkably finely tuned for life, does this not (strongly) suggest that the universe is ontologically haunted and that this fact should require further exploration, given the metaphysically staggering implications?
Nobody knows whether or not the matter and energy began to exist a finite amount of time ago. We think it existed as a singularity, a region of infinite density and infinite space-time curvature. What happened before that is potentially a meaningless question given that the big bang (i.e. the expansion of this singularity) is when we think time, as we know it, began.
And "the universe is fine-tuned for life"? No. Life is fine-tuned for the universe, or at least our tiny corner of it.
Granted that the major objection to belief in God is the problem of evil, does the concept of evil itself not suggest a standard of goodness or a design plan from which things deviate, so that if things ought to be a certain way (rather than just happening to be the way they are in nature), don’t such ‘injustices’ or ‘evils’ seem to suggest a moral/design plan independent of nature?
I don't accept that "the problem of evil" is the main objection to the belief in God. There are many other factors, and every atheist has come to his or her conclusions via different thoughts and concepts. For me in particular, it's the complete lack of any evidence. And no, I don't believe that the fact that we can recognize an act as "evil" means that there must be an objective standard for "good". This is like saying that because I find olives to taste bad, there must exist somewhere a food that tastes absolutely perfect.
Please explain how something can come from nothing, how life can come from non-life, how mind can come from brain, and how our moral senses developed from an amoral source.
As I said above, the big bang theory does not require something to come from nothing. It describes the universe coming from the singularity, which may have always been there, or may have come from somewhere else.
Life could come from non-life via molecules such as RNA strands or something similar, which, since they can self-replicate, can undergo the process of evolution and selection.
How can mind come from brain? I'm not sure how you define the word "mind" but I assume you mean consciousness. I believe that consciousness is an illusion resulting from electrical impulses in our material brain.
Our moral senses likely arose as a by-product of our evolutionary history.
These explanations, I believe, are plausible. The details are being fleshed out more and more each day by scientists and experts the world over. The amount of evidence for the truth of these ideas is growing. And they require no god or supernatural elements to work.
It should also be pointed out that theists certainly cannot answer these questions any better than I can, at least not beyond "God did it", which explains nothing at all.
Irrespective of one’s worldview, many experience periods of doubt. Do you ever doubt your atheism and, if so, what is it about theism or Christianity that is most troubling to your atheism?
I honestly never, ever doubt my disbelief in any of the organized religions, or of the concept of a personal or intervening god.
Why is something here rather than nothing here? Clearly, the physical universe is not eternal (Second Law of Thermodynamics, Big Bang cosmology). Either everything came from something outside the material universe, or everything came from nothing (Law of Excluded Middle). Which of those two is the most reasonable alternative? As an atheist, you seem to have opted for the latter. Why?
This question seems to be built on several unfounded assumptions. The idea that "the physical universe is not eternal" is not "clear" to me. Then, "everything came from outside the universe" or "everything came from nothing"? These are not the only options. How about "everything was always here, in some form of other"? The big bang theory does not refute this, and if something had to have always existed, it might as well be the universe than God. And an atheist is a person lacking belief in a god. The descriptor "atheist" says nothing about a persons belief regarding the origins of the universe any more than about their taste in music.
If our cognitive faculties were selected for survival, not for truth, then how can we have any confidence, for example, that our beliefs about the reality of physical objects are true or that naturalism itself is true?
Much of this question can be discarded. It boils down to "How can we believe in anything?". This question should be more unsettling to the theist than the atheist. The answer is that, philosophically, we can never be certain about anything, but we can test ideas by repeat measurements, theories, models and verification of predictions. God fails these tests, whereas my hypothesis that "if I drop a brick on my foot, it will hurt" is based on past experience and my knowledge of the world. Science works.