Is John 3:23 contradicted by 1 John 4:5-6? Does the born again experience happen by the Holy Spirit or by both the word of God/Gospel and Holy Spirit? Is John 3:23 contradicted by 1 John 4:5-6? From this comes following: does the born again experience happen by the Holy Spirit or by both the word of God/Gospel and Holy Spirit?

And he said unto them, Ye are from beneath; I am from above: ye are of this world; I am not of this world. (John 3:23, KJV, emphasis mine)
They are of the world: therefore speak they of the world, and the world heareth them. We are of God: he that knoweth God heareth us; he that is not of God heareth not us. Hereby know we the spirit of truth, and the spirit of error. (1 John 4:5-6, KJV latter)

This site claims that John 3:23 refutes LDS claim of pre-existence.
The most important thing when interpreting a passage is the context:

John 8:21-23 ESV So he [Jesus] said to them [Pharisees] again, “I am going away, and you will seek me, and you will die in your sin. Where I am going, you cannot come.&quot; So the Jews said, “Will he kill himself, since he says, ‘Where I am going, you cannot come’?” He said to them, “You are from below; I am from above. You are of this world; I am not of this world.
1 John 4:2-6 ESV By this you [John's disciples] know the Spirit of God: every spirit that confesses that Jesus Christ has come in the flesh is from God, and every spirit that does not confess Jesus is not from God. This is the spirit of the antichrist, which you heard was coming and now is in the world already. Little children, you are from God and have overcome them, for he who is in you is greater than he who is in the world. They are from the world; therefore they speak from the world, and the world listens to them. We are from God. Whoever knows God listens to us; whoever is not from God does not listen to us. By this we know the Spirit of truth and the spirit of error.

[bracket stuff added by me]
Do these passages contradict? Not at all--in fact their ideas are almost identical.
Jesus was telling the Pharisees that they were from below--from the fallen world. They refused to believe in him and he was identifying that as a belief from below. Contrast this with 1 John, which is saying the same thing to a different crowd. John is saying a belief in Jesus as the savior is a belief (spirit) from above. John is reinforcing Jesus' words.