There is no "separation of church and state" clause in the first amendment. There is a "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof" clause. In other words congress cannot establish a state religion, nor can it prohibit you from exercising whatever religion an individual adheres to.
The very first Congress of the United States, opened with prayer, so to imply that the founding fathers original intent was to eliminate religion ("separation of church and state") is a false claim. Note the offering of a prayer does not "establish a state religion" nor does it proscribe rules of acceptable behavior or any actions of worship.
Samuel Adams, the Father of the American Revolution, "arose," according to John Adams' account, "and said that he was no bigot, and could hear a Prayer from any gentleman of Piety and virtue, who was at the same time a friend to his Country." (Note to the ACLU: according to this Founder, opposition to public invocations is a form of bigotry.)
As a result of Sam Adams' intervention, the motion carried and an Episcopalian clergyman, Rev. Jacob Duche', was prevailed upon to open the next morning's session in prayer.
Following the reading of Psalm 35, according to Adams, quite unexpectedly, because it was not the custom of the day, Rev. Duche' launched into a spontaneous and unscripted prayer.
His prayer began, "Be Thou present, O God of Wisdom, and direct the counsel of this Honorable Assembly; enable them to settle all things on the best and surest foundation; that the scene of blood may be speedily closed; that Order, Harmony, and Peace may be effectually restored, and that Truth and Justice, Religion and Piety, prevail and flourish among the people."
Duche' went on to ask God to preserve the delegates' health and vigor of mind, and to grant them "temporal Blessings" and "everlasting Glory in the world to come."
Rather than being scandalized at this "sectarian" prayer, Adams writes that Duche's prayer "filled the bosom of every man present. I must confess, I never heard a better prayer, or one so well pronounced."
It was prayed, he went on, "with such fervor, such ardor, such earnestness and pathos, and in language so elegant and sublime, for America, for the Congress, for the province of Massachusetts Bay, and especially for the town of Boston. It had an excellent effect upon everybody here."