I didn't see stigmata, though I do believe that there is such a phenomenas. Just as with many strong beliefs, it can cause such miraculous things to happen. Happens in other societies with different beliefs as well.
As far as people going to church to honor Jesus, it would be cool if people actually did listen to his words, but instead they follow Pauls teachings more than Jesus. If only the Bible would be revamped and only consisting of the words of Jesus.
I assume you are referring to this particular verse:
The kingdom of God is within you and all around you. It is not within buildings of wood or stone. Split a piece of wood and you will find me. Look beneath a stone and I am there.
by St. Thomas. He is arguably the most popular chronicler of Jesus (outside organized Christianity). The Gospel of Thomas is a listing of 114 purported sayings of Jesus that emphasize the divinity within each person. Gnostic texts were found to be so threatening that many were destroyed or hidden, only to be rediscovered two thousand years later. Many of the gnostic concepts contradict the common Christian doctrine.
Prove "mary magdalene was supposed to take over when jesus died but paul and some of the other apostles were jealous of mary's closeness with jesus."
As far as I know, the only source that quotes Jesus as talking about future leadership is, coincidentally, the Gospel of Thomas, and there he says that his brother, James the Just, should lead the church.