Excellent post John!
I love it when folks take the time and effort to articulate their position with clarity.
There are many points that I would like to address, but I want to take them one at a time since otherwise the posts become unwieldy.
Before giving my first response, I want to acknowledge the points you made in your closing paragraph. The Bible is an exceedingly rich book that does not really have a peer in other religious texts as far as I know. The Tanakh can't compare because it is incomplete relative to the Bible. It doesn't form a complete story. Indeed, it ends with the destruction of Jerusalem in 586 BC (2 Chronicles) with the promises clearly unfulfilled. And the Quran can't compare because it is mostly just a confused mish-mash of Bible stories. The Book of Mormon is fraudulent. The only serious contenders would be the Eastern texts like the Vedas, Upanishads, and Buddhist scriptures. Unfortunately, I don't really know enough about those books to make a judgment at this time, except to say that Buddhism is atheistic so it can't be from God (in the sense of theism, i.e. a personal God). So if there is any book produced by God, then it is seems most likely the Bible. But the problems with the Bible and the concept of theism have convinced me that there probably is no "Book of God" at all. And as we will see in our discussion of your post, the things you take as "answers" are to me reasons to reject the Bible.
I will begin at the top of your list, Origins:
(1) From whence came substance?
(2) From whence came life?
(3) From whence came death?
(1) I don't think it would be fruitful to discuss point #1 at this time for three reasons. 1) I was trained in Physics and Mathematics so the conversation would probably be lopsided. 2) The question is very philosophical with no certain answers so it wouldn't really help to discuss it. 3) There are much bigger fish to fry in your other questions.
(2) I don't see the Bible as giving an adequate answer on this point. Indeed, I believe it gives a demonstrably wrong answer, and that is one of the reasons I can't believe the Bible is from God. Have you studied evolution at all? Have you read any books that explain the evidence? If not, you have probably been misinformed by Christians who are deceiving people about the topic. So the first question I would like to ask is this: Are you familiar with the evidence for the common descent of all living creatures? It comes in a variety of forms such as the morphological tree of life which also is confirmed by DNA analysis of the same kind courts accept as evidence of paternity. This is why the case is so strong. We have solid evidence that all organisms are biologically related to each other in the sense of having a common ancestry.
(3) The Biblical explanation of death is also very problematic. It looks like pure mythology. Magic trees, talking snakes, etc. Death does not need an explanation. It is impossible to conceive of a physical world in which death didn't happen because organisms are made of atoms, and any compound object can be destroyed. This was Buddha's last words "All compound things are subject to dissolution." I don't see how it could be any other way unless God constantly overrode natural laws.
I can't trust the Bible because the whole creation story which describes our origin is riddled with problems. There was no creation of Adam and Eve and all the animals a mere 6000 years ago.
Well, that's enough for a start.
Thanks again for a great post.