Great questions - I don't claim to be an expert, but this is my experience.

I found myself in a similar position, and ultimately came to an important realization: the Christian faith is as much experiential as it is intellectual. When you examine every belief system - from Christianity, to Islam, to Atheism - there will be gaps and holes in each of the doctrines, leading to lingering questions in all contexts. Stated simply, an analytical approach will inevitably lead to a less-than-certain answer about absolute truth.

From a certain perspective, however, doesn't this make sense? If Christianity could be conclusively defended through human logic and reasoning, what would be the importance of faith? Essentially faith would become superfluous: I instead choose to follow God because every "t" is crossed and every "i" is dotted. Such skepticism hardly reflects the emphasis that the Bible places on putting one's trust in God, despite the presence of doubts. "Blessed are those who believe without seeing me." John 20:29

The obvious rebuttal is that such an answer is a cop-out; indeed, it would be difficult for anyone to refute the argument that "all you need is faith!" So at this point, I just prayed - with faith - that God would reveal himself to me, and man did He deliver.

I think Martin Lloyd Jones best described what I felt, "The fuses of love are so overloaded they almost blow out. The subconscious doubts—that he wasn't thinking about at the time, but that pop up every now and then—are gone! And in their place is utter and indestructible assurance, so that you know that you know that you know that God is real and that Jesus lives and that you are loved, and that to be saved is the greatest thing in the world. And as you walk on down the street you can scarcely contain yourself, and you want to cry out, "My father loves me! My father loves me! O, what a great father I have! What a father! What a father!"