So how does the Universe really work

Up to now, most scientists have been too occupied with the development of new theories that describe what the universe is to ask why. On the other hand, the people whose business it is to ask why, the philosophers, have not been able to keep up with the advance of scientific theories.... Philosophers reduced the scope of their inquiries so much that Wittgenstein, the most famous philosopher of the twentieth century, said, 'The sole remaining task for philosophy is the analysis of language.' What a comedown from the great tradition of philosophy from Aristotle to kant!

If we do discover a complete theory, it should it time be understandable in broad principle by everyone, not just a few scientists. Then we shall all, philosophers, scientists, and just ordinary people, be able to take part in the discussion of the question of why it is that we and the universe exist.-A BRIEFER HISTORY OF TIME by Stephen Hawking and Leonard Mlodinow

This year I have read three books trying to upgrade my physics knowledge and my understanding of the universe. I have enjoyed the topic, but it reminds me of how much still can't be explained, and maybe never will be. Granted my knowledge of Higgs boson and string theory is a little thin. That being said, here is a short list of that which amazes and confuses me.

• The two most complete theorems for how the universe works are General Relativity and Quantum Physics. The former doesn't account for the quantum uncertainty principle and the latter doesn't explain the force of gravity. Our two best explanations for the universe contradict each other. In spite of that experiments designed around each theories are consistently prove specific aspects of each of them independently.
• The Universe is both expanding and accelerating. What force is causing the acceleration?
• The Universe looks the same in all directions. All of the galaxies seem to be moving away from ours. The background radiation from the big bang comes from all directions. Are we in the center of the universe? What are the odds of that?
• Experiments with electron refraction show that a single electron when moving takes all possible paths at the same time. How does that work?
• Einstein shows that speed and gravity affect time.  The GPS satellites orbiting the earth hold highly tuned atomic clocks. Since the clocks are farther away from the earth, time moves faster for them.  These satellites have to be adjusted according to the theory of relativity. If they weren't the clocks would be off by 45 microseconds a day (10 KM of accuracy in a GPS fix) http://www.astronomy.ohio-state.edu/~pogge/Ast162/Unit5/gps.html
• String theory also seeks unlikely to explain the universe. There are too many dimensions needed to make it work, and I'm a little hung up on that. But I haven't yet read that much on the topic yet.

If anyone has any recommendations on higgs boson reading let me know.