The phrase "Split a piece of wood; I am there. Lift up the stone, and you will find me there." comes from the "Gospel of Thomas" (Verse 77).
When Father Kiernan (Gabriel Byrne) comes in the Vatican office to get his new assignment, audience can hear a bit of Italian speaking in the back between Cardinal Daniel Houseman (Jonathan Pryce) and another priest. Translation: "Rest assured, none of this will ever leave this room."
The Gospel of Thomas is a historical document that some believe to be the words of Jesus to his disciples; however, the actual document was written in Coptic, an ancient Egyptian language based on the Greek alphabet, not Aramaic, as the movie states.
The "Aramaic" Frankie writes on the wall is in fact ancient Hebrew, which Rupert Wainwright thought looked more intriguing.
Patricia Arquette's character is named Frankie (short for Frances), similar to the name of the saint, Francis, whom we're told by Gabriel Byrne's character was the first to receive the stigmata.