Where did all that matter and energy come from?
Matter
Energy
What caused its release?
See above
How did this explosion of everything (from nothing) order itself?
It evolved over billions of years. What we see as the universe today is not what it was 10,000 years ago.
Where did the chemical elements come from?
Chemical elements
Where did the mathematical laws and physical properties come from?
Those are inventions of man to descibe various actions and reactions of the atoms that make up our world
Where did the information code in DNA come from?
DNA wasn't invented - it was always there and was only semi-recently discovered and the ability to "read" it was invented.
Where did the language convention that interprets DNA come from?
Not sure what you mean by this. All language was invented by man, whether it be computer code, verbal communication or DNA interpretation.
How do we explain the design, complexity and fine-tuning inherent in spiral galaxies, solar systems and stars?
They evolved over time. See the answer to "explosion of everything".
How did life come from a rock?
I was unaware that life did come from a rock. Cite your source, please.
How did a bird come from a lizard?
I thought the theory was that lizards came from birds. But "evolution" would be the answer.
Why don't we see birds come from lizards today?
Live a million years and maybe you will.
Why are there no transitional fossils at all?
There are plenty of transitional fossils on record.
Why have we never observed beneficial mutations?
Are you crazy? What do you call our natural immunities? People used to die of the common cold and now they don't. What do you call giraffes, who mutated in order to feed from the tops of trees where the other animals couldn't reach? What about black people developing dark pigmented skin to keep them from frying in the African sun?
Explain the random development of the human eye, reproductive system, digestive tract and brain?
Evolved over billions of years until it became what works and what we recognize today. And it will continue to evolve - if you suddenly woke up a million years in the future, humans would be dramatically different than they are today.
What about the subconscious mind?
What about it?
What about love, morality, ethics and emotions?
Those are mergings of physiological and psychological traits. Your brain fires neurons and chemicals in response to certain stimuli, and your history (the "nurture" part of the "nature vs. nurture") tells you to recognize those biological instances as "love" or "hate" or whatever. What causes an emotional response in you will not cause an emotional response in everyone - you were taught to respond that way.
Morality and ethics are taught, not intrinsic. And I give you any number of criminals to support that statement.