Lyric discussion by Artemistry 

I think the John or Paul reference, refers to biblical literature written by both. The Gospel of John and then the Pauline letters (my dad's a preacher too, and I had to go to Xian school). I think the basic gist of this line is that different parts of the bible ("Gospel") were written by different men who had different agendas. There is, in the Nag Hammadi (lost biblical books) a book entitled "The Gospel of Mary Magdalene", and I think the other comments are correct that this book is about Mary Magdalene (there are those who believe that she and Jesus were married, hence "Mrs. Jesus"). In this book, Mary Magdalene is considered the most beloved by Jesus.

Of course, I could be completely wrong, and it is a reference to the Beatles.

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