What is the origin of "Separation of Church and State" doctrine?

The "wall of separation" was a metaphoric construction of the First Amendment, which Jefferson time and again said imposed its restrictions on the national government only (see, e.g., Jefferson's 1798 draft of the Kentucky Resolutions). ... The First Amendment, as originally understood, had little substantive content apart from is affirmation that the national government was denied all power over religious matters. Jurisdiction in such concerns was reserved to individual citizens, religious societies, and state governments....
"Origins and Dangers of the "Wall of Separation Between Church and State" by Daniel L. Dreisbach, Professor of Justice, Law, and Society at American University (Article in Imprimis, published by Hillsdale College)