Kinyan 41 Misyashev Libo B'Talmudo - Between The Vilna Gaon & Rav Zemele Volozhin
The story is told that once Rav Chaim Volozhin, after extolling the greatness of his brother Rav Zemele Volozhin a talmid of the Vilna Gaon, was asked what is the difference between the Torah knowledge of his great Rebbi the Vilna Gaon and that of his brother . He said we all know Ashrei by heart, but can we say it backwards? Do you know the word before the pasuk that starts "Tov Hashem"? This would need to be figured out by starting from the pasuk before until you reach the last word. Not so with the Vilna Gaon. He saw the whole Shas before his eyes and can tell you anything. It was like reading from an open book that is in one's mind.
It is not enough to go through Shas or even learn it. It must be in your bloodstream and your bones. All concepts in the gemara are unfamiliar to us even after learning it. They need to become second nature. You need to learn it until you know it inside out. In order to gain a grasp of one's learning one must understand the rationale that hides behind the simple meaning of what we are learning. The Amora Shmuel said (Brachos 58b) "Nehirin Li Shvilin D'Shmaya K'Shvili D'Naharda'a", the pathways of the sky are clear to me like the streets of my hometown. That is how familiar we must become with the avenues and alley ways of Shas.
How is this done? Borrowing an idea that the Kotzker Rebbe said about Yiras Shamayim we can see this in the pasuk in 'V'Haya Im Shamo'a' that says, 'V'Samtem Es Divarai Eileh Al L'vavchem', it doesn't say to put torah in your heart rather to place it on your heart. Our hearts are hardened and closed to us from all the abuse. What we can do, is take torah that we have learnt and put it on our hearts. Then one day when our heart opens, however momentarily, it will all fall right in. We need to keep on learning and reviewing. Then suddenly one day in a Sha'as HaKosher the gates will open up and you will deeply absorb all the torah you have toiled to know for years.