Have a read of this post (and follow the link). (The link with viscera is not just a metaphor, by the way.)
I too have been fortunate in finding my place within a tradition that is balanced, hence when I was outgrowing my atheism, I could grow in faith without having to leave behind my sceptical intelligence. Hasn’t always been easy though. At a time when I was struggling the most with my faith (second year of priestly training, believe it or not) it was reading Jacques Pohier’s book ‘God in Fragments’ – about his breakdown and renewal of faith (he was a Dominican priest) – that brought me back from the brink.
This is why it is utterly essential for doubt to be embraced within the church, and for questioning to be affirmed and valued. We cannot exist if we are afraid of the truth. Faith and doubt are not opposites, they are siamese twins (as I keep saying). The opposite of faith is fear.