Hey there L & R,
Welcome to the board.
I went through a very similar transformation. What really helped me the most was going back to school shortly after making the big exit. The Borg's oppressive attitude toward knowledge and education made me crazy and I was thirsty for as much knowledge as I could consume. I majored in geology and got my BS in 2004. Now I am nearly finished with a masters in geology and a law degree, but the geology education means the most to me. Geology and astronomy are the two sciences that deal with the concept of "deep time" -- 100s of millions to billions of years.
You simply cannot think about those vast expanses of time without questioning everything about where humans came from and where we fit into the evolutionary history of the earth. I too am not an atheist, but rather I consider myself an agnostic. My experience with the hard sciences has taught me to apply the scientific method to evaluate things. Nothing in science is ever really "proven" but, instead things sit on a continuum between false and true. As science progresses and hypotheses and theories are tested they are pushed toward one end of the continuum or the other.
On the faith continuum, with 0 = "no doubt/full faith" and 100 = "complete doubt/no faith," I am probably at about 99.5. I can't go to 100 because I feel that is just as presumptuous as the person who is at the other end of the continuum with full faith. On the other hand, I don't really don't expect anything to draw me below 99.5, but I am always open to ideas.
When I was going through my transformation from Dub to Agnostic it was a very scary experience. Almost like stepping off of a cliff in the dark and not knowing where I was going to end up. However, I can honestly say now that I have the greatest calm and peace of mind I have ever had.
Good luck, you are well on the way to an enriched life.
All the best,
Alex