Trying to answer this without writing a book is more difficult then I expected.
I'm not a Christian therefore I don't believe in any biblical stories. Instead, I believe that they are stories based on folk lore, a way to established rules and order, or significant events of the past. (IE. Noah's Ark was not Noah's Arc but rather the flooding of the what? Dead Sea? or Red Sea? I'm more tired then I thought.)
However, I'm not atheist due to the fact that I rely heavily on science as well. The theory that energy/matter cannot be created or destroyed interferes with the "creation" of the universe. How it came to be, I don't know.
I also believe we have souls. But I also think that we rely and function heavily on energy. That would be where my belief in quantum physics comes in to play - hence quanta.
I also believe things happen for a reason. I don't think things are pre-destined and we cannot change our destiny - I believe we have all control over our destiny by our choices. However, I think our choices or the way things are brought to us happen for a reason.
It is rather difficult, yes!
As far as the biblical stories go - I agree with you in many points as far as the Old Testament goes (I am pretty liberal) in that many contain religious and symbolic truth rather than literal truth. I think some others are simply products of historians getting a bit excited by good events and then trying to explain why s*** happens for bad events. The new testament... I believe there are probably a few points that are just a tad skewed and patched; however, I choose to follow by the example of the book (Christ) rather than the book itself - this message is love and I prefer to follow that rather than a rather homophobic St. Paul for example!
Your beliefs are very much like that of a Buddhist I think you would be surprised to hear! I would really suggest that you do some reading up as I think you could really gel with their philosophies if you wanted to...
I do have to pick you up on the part of how the Law of Conservation of energy/matter disrupts with teachings of God the creator. I explain this in the following way; this is not my own philosophy I might add but someone else's which I think is rather good!
If we look back to Genesis we find that it is actually quite possible that God did not create matter and energy himself but this too pre-existed; however he did 'form' and 'shape' the universe in such a way as could easily be considered 'creation' - just not in the same manner as one would expect. I may also point out that God did still create something (matter) out of what is effectively nothing - energy is formless, massless and chargeless; practically non-existent.
To look at Genesis:
1 In the beginning God created the heavens and the earth.
2 Now the earth was formless and empty, darkness was over the surface of the deep, and the Spirit of God was hovering over the waters.
3 And God said, "Let there be light," and there was light. 4 God saw that the light was good, and He separated the light from the darkness. 5 God called the light "day," and the darkness he called "night." And there was evening, and there was morning—the first day.
As you see form the first verse it would seem obvious that God created everything. However, if you take a closer look the first verse seems more of a summary as it then goes on to actually explain the process of the 'creation'. Also if you look at the actual wording used in the 2nd verse it does actually seem oddly similar with the view of creation - nothing of substance then substance has arrived.
As a sidenote; it is possible that the universe is actually a part of God. If you look further on you will see that God need only will things to happen for it to happen - this would indicate that God has complete power of the universe which I would argue could only come from it actually being a part of God.