The error that pervades your entire post is the assumption that reason is supreme, whereas it is not. The assumption of the believer is that some things are unfathomable rationally because God is Infinite and we are finite. We cannot rationally grasp Infinity in toto, therefore faith is the alternate approach to God, not arrogant reason that must lead ultimately to agnosticism.
For the atheist reason, not faith, is supreme. Yet ultimately he, like the agnostic, falls prey to the belief that the universe we live in is irrational and meaningless. This is a logical conclusion to draw since he refuses to entertain the belief that the universe was created by God for a reason. The atheistic and negative existentialism of Nietzsche, Sartre, and Camus lend support to this view.