Having watched your debate with Michael Shermer on the existence of God, I wish to commend you for your ability to grasp the point of an argument with great accuracy, which is the characteristic of a good debater. On the idea of God creating the universe, as I mentioned in my earlier email to you, I'm an atheist: I believe in a universe without any purpose created entirely by physical, natural processes. But if I were a theist, my stance on it would be very much like yours, though with a slight difference. I appreciate you in reconciling your faith with science (unlike those anti-science Bible literalists who believe the earth and the universe are less than 10,000 years old, thereby denying reality). However, there would by a small difference between both our stances. Instead of always keeping my God just one level ahead of the reach of current scientific paradigm and concluding that 'X' was a natural process brought about by a supernatural 'Y,' I would assume that 'X' was a natural process brought about by a natural 'Y'. But I would also conclude that every single natural process that has ever taken place in the history of the universe and every natural process that eventually led to the creation/birth of the universe was intended by a supernatural God. With this outlook, I can reconcile every scientific discovery and every successful scientific theory with my faith without ever having to fear science discovering something that contradicts my faith. This stance would also convince me why God has not left behind any physically testable evidence for His own existence, but has instead left behind an entire universe that stands as testimony to His intent, without Him ever having to physically intervene with the natural universe. As you can see, there is only a tiny difference between this stance and your stance, though both stances reconcile science and faith. But this tiny difference makes all the difference in accepting and denying science. As the great physics Nobel Laureate Steven Weinberg so eloquently put it, "Science doesn't make it impossible to believe in God, it only makes it possible to not believe in God."
Your email is very interesting, and I agree nearly entirely with what you have expressed.
If you were a theist, you write, your approach to science would be the same as mine. We both reject the "god-of-the-gaps." I look at the entire process and see it as the hand or plan of God. You look at the entire process and can envision it being the hand of God.
Even though you are an atheist, we appear to be even closer than you think!