I, too, have many doubts, pretty much all the time. As I wrote before, particularly in my exchange to JNorm about Bill Maher, I was raised that way, raised in the wonderful intellectual, secular-humanist culture that nourished the "Intelligentsia" of the old Soviet Union. My parents were scientists, my grandma was a librarian, my great-grandfather was a teacher of Latin and Greek in the old Zarist "Gimnazija," etc. In my family, there has always been a cult of books, knowledge, intellectual honesty, scrutiny, and doubt. Every cell and molecule of yours truly is sharply against any blind belief, any indoctrination, any brainwashing. That was a life-saving thing in the old Soviet totalitarian regime, and I keep it now. My wife and daughter are that way, too, and all of our friends (at least old, trusted lifelong friends) are that way, too.
But, like others have already said above, all my doubts, as far as the Orthodox faith is concerned, become very secondary, indeed, when I go to a Divine Liturgy - or, perhaps broader, when I participate in the liturgical LIFE of the Church. I can think critically about writings of some Father all week (or even month) long. But early in the morning, when I am standing in front of my icons and say, "Lord Jesus Christ, by the prayers of Your Most Pure Mother, and of our Holy and God-Bearing Fathers, and of all the Saints, have mercy on us!" - I have a rather peculiar, irrational, un-explainable feeling. It is a feeling that it all is really so: that right now, in "heaven" (even though we don't know what it is) there exist all these Fathers (no matter what I think of their particular writings), and all these saints, all these holy, worthy people who lived, struggled (harder than me!), and are now seeing Christ, literally sitting at His banquet table. This same feeling, greatly aughmented by the liturgical tunes, colors of the icons and of the priestly vestments, candllelight, and incense, comes to me during the Divine Liturgy in my tiny mission parish in the middle of the rural Mississippi nowhere, or downtown Kyiv, when I visit home.
To me, it is that irrationality, that mystery of the Church that keeps drawing me to God and away from my own little caprices and lusts.