What is the meaning of the verse: "When Allah said: 'O Jesus, indeed I will take you and raise you to Myself'", and does it indicate that Jesus, peace be upon him, is with Allah the Almighty above the seven heavens, and how can this be reconciled with his presence in the second heaven?

There is no contradiction between the presence of Jesus (peace be upon him) in the second heaven and the Almighty's saying: "and raising you to Me," for texts explain each other. The word "to" does not imply spatial mixing but indicates the direction of loftiness and the place of God's honor. Imams have used this verse as evidence for God's exaltedness and His establishment upon His Throne. The raising of Jesus (peace be upon him) was generally to heaven, and the Quran did not specify which heaven, while the Sunnah pinpointed his location in the second heaven. This is a detail for what was summarized in the Quran, not a contradiction to it.