"Lincoln's Battle with God" (Stephen Mansfield) - This is a biography of Lincoln focusing on his religious life. I found it rather frustrating, but I think that is the nature of this area of historiography more than any lacking in the author.
As the author states in his conclusion: we want a clear story; with a beginning, middle, and end. An aisle walked, a bold profession. But life is messier than that, and the life of the President during what is likely the messiest time in America is messy.
Perhaps the greatest revelation of Lincoln's journey is from his last public proclamation: "The Almighty has His own purposes."
Now, on the face of it, this seems a pretty abstract statement. However, as we look at Lincoln's life as a whole, we can see that he struggled most with the sovereignty of God and the hardship of life (the problem of evil).
Lincoln was born into an ostensibly Christian culture, that showed much of the shallowness and hypocrisy we see today. His father was some sort of hyper-Calvinist - refusing to bring his son up in the fear and admonition of the Lord, and showing little Christian behavior. His mother seems to have been more faithful, and likely instilled a lasting binding to the Word which Lincoln would hold to even in his lowest moments.
It's easy to see how such an environment could lead to his atheist phase. There was a surge of secular and atheistic writing at the time, and they were far more consistent than the Christians he had encountered.
But atheism has no lasting strength, and Lincoln needed that. He faced death almost continuously: losing siblings, parents, friends, and later children (not to mention the horrors of war). He needed answers, and he kept looking.
It would seem he found those answers. He remained wary of organized religion, but he seems to have come to know God in Jesus and to trust Him.
His wife, Mary (who was no strong Christian, dabbling in mysticism and spiritualism), says his last words were "We will visit the Holy Land and see those places hallowed by the footsteps of the Savior. There is no place I so much desire to see as Jerusalem."