As for John 1:1, I include it in some of my discussion on my Mormon Answers page on relationships between God the Father, Christ, and man. An interesting insight is given by Russell C. McGregor and Kerry A. Shirts, "Letters to an Anti-Mormon," FARMS Review of Books, Vol. 11, No. 1, 1999, p. 139):
In John 1:1-2 we read, "In the beginning was the Word, and the Word was with God, and the Word was God. The same was in the beginning with God." ... [T]he first and third "God" in this passage comes from Greek Ho Theos - the God - while the second occurrence was simply Theos. So this could be rendered, "In the beginning was the Word, and the Word was with The God, and the Word was God. The same was in the beginning with The God."In my opinion, John 1:1 actually supports the notion that Christ and the Father are not the same Being. That's why, for example, Stephen could see Christ standing at the right hand of the Father (Acts 7:55-56). That's why Christ could say that His Father is greater than him (John 14:28). But they are one.
For further information, see my page, "What Mormons Believe About the Oneness and Unity of God."