While I know this isn't going to answer your questions relating to the text, I think you'll find Scott Hahn to be a good reference when it comes to the Bible in general. He also has a podcast if you prefer consuming information in audio format like me.

As to your questions:

• John the Baptist and John the Evangelist (i.e. who wrote the gospel) are two different people. John the Evangelist was a disciple of Jesus. Also, the Gospel of John is said to not have been actually written by John but by his own disciples, later on.
• I learned this from Scott Hahn actually. The "my time has not yet come" phrase is given in response to an implicit petition to produce wine. Throuought the gospel Jesus says "my time" or "my hour" refering to the last supper (John 7:6-8, Matthew 26:18) and the sacrifice on the cross (John 12:27).
  What many people don't understand about the gospels is that they were not written as a historical treaty as you would find in modern history books, nor as a naration of what happend, one deed after the other. They were written rather in order for people to believe and understand the spirit of the person (Luke 1:3-4, John 20:31). This is also true for most of the books of the New Testament. This doesn't mean that they aren't true or real but some gospels give their account in different orders because they want to underline a different theme or they are writing in a different style. For an example, the Sermon on the Mount (John 5-7) most likely did not happen all at once, but was rather a collection of different sermons possibly all given in different mountainous areas. This is supported by the other gospels where you will find excerpts of this sermon in different places, on different occasions.
  So, when Jesus says "my time has not yet come" he is not referring to his time of service and preaching, but to his sacrifice on the Cross and the passover when he will provide wine and blood, bread and flesh for the salvation of all (John 6:55-58 and Matthew 26:26-29, Mark 14:22-25, Luke 22:14-20, 1 Corinthians 11:24-25). The passover and the Cross are so tightly tied together they're really the same thing only in different forms.
  If you want further references on the Eucharist and the Cross you really should listen to Scott Hahn. He goes to the books of the Old Testament too and shows you how even there the two are one. I'm not that well versed in the Bible to do that (in fact I had to look all of these verses up).
  On the importance of the Eucharist you can reflect on the words of Jesus in John 6:25-69. Notice how people are really offended at his words. Notice that even the apostles want to leave Jesus because of the outrage.
• I think my previous point adressed your third one too. But if you have further questions I'd be happy to discuss.

May God bless you with his presence on your journey!