Was John the Baptist Elijah? There is really a verse that is missing from this page, and that's Luke 1:17,
And he shall go before him in the spirit and power of Elias, to turn the hearts of the fathers to the children, and the disobedient to the wisdom of the just; to make ready a people prepared for the Lord.Generally, when there's confusion over a matter in the Bible, you go by what Jesus says. Jesus said John was Elijah (less directly in Mark 9:12), so he was. So why the confusion? Well, one explanation that I have heard--and I don't know how widely accepted this is that the spirit of Elijah was reincarnated in John, but John had no memory of his previous life. Strange to talk about reincarnation in a Christian context, I know, but I've heard it suggested, and it seems to fit the Luke verse.
Where did John baptize? on the face of it, there's no contradiction here, as "beyond Jordan" most likely simply means in the Jordan River, but on the east bank. However, there is the issue raised not on the linked page, but back in the footnote on the John 1 page, which points out that Bethabara (Βηθανια in my Greek version) is not known. My study guides say that "Bethabara" is Hebrew for "ferry-house" which would suggest perhaps that this was not so much a city as simply a place where one could cross the Jordan.
Did John the Baptist recognize Jesus as the Son of God? Yes, but obviously, some explanation is needed here. The verses in the "no" column are coming from John when he's locked away in prison. While he recognized Jesus's true identity at his baptism, he has to be wondering, if the Messiah has come, what am I doing behind bars? There are a couple of possibilities for this message here. One is sarcasm; John is calling out to Jesus and saying, "Hey, I'm in trouble! Are you the Messiah or not?" The other is desperation: because John is in this situation, he's starting to question himself and what he thought he saw. Either way, it's not really a contradiction.
Which came first: the calling of Peter and Andrew or the imprisonment of John the Baptist? There are two things that need to be said about the content of this page, and either or both could explain it. First of all, it should be noted that the so-called "calling" of Peter and Andrew here in John is not the same event shown in the other two Gospels; they look different, and I believe the events in Matthew and Mark happened later. It's worth observing that the behavior displayed by Peter and Andrew isn't the sort of behavior you would expect from people who didn't already have a history of interaction with Jesus; you don't just walk up to a stranger and say, "Follow me!" and have them come. The event in John's Gospel is just some of the people who would later be his Apostles meeting Jesus for the first time. They are "following him" in the sense that they want to see where he goes and what he does, not in the sense of yet being dedicated disciples. The second thing that needs to be said about John's Gospel in general is that John is not really trying to tell a linear story. Until we get to Palm Sunday, John's Gospel is just a bunch of stories thrown together in no particular order; once get to Holy Week, John is more concerned with getting events in order.
How did Peter find out that Jesus was the Messiah? This is actually a matter of understanding the difference between what's going on between these two verses. Yes, Peter's brother told him that Jesus was the Messiah, but I think the difference is that by the later time that Jesus is talking in Matthew 16, Peter had truly internalized the truth and fully believed in him. I mean, if you think about it, if someone just told you, "Hey, there's this guy, and he's the Messiah!" you would probably check it out, but questioningly. After you had been with Jesus for a while, heard his teaching and seen his miracles, you wouldn't be questioning any more.
How did Peter and Andrew become Jesus's disciples? Part of this I answered above: the story in Matthew and Mark happened later than the story in John. However, how does the story in Luke fit in? There are two possibilities. One is that Luke is simply telescoping events and Peter follows Jesus after this event, but not necessarily immediately. The other, which seems more likely to me, is that Luke is giving greater details of the story than Matthew and Mark did. This may be a bit strange, because as I may have noted when I went through Mark, it's generally understood that Mark's Gospel is largely made up of material Mark got from Peter.
Where did Peter and Andrew live? This is definitely unclear, but one thing that can be said about this inconsistency is that Capernaum and Bethsaida are right next to each other at the north end of the Sea of Galilee. If I had to venture a guess, I'd say it's more likely Mark made a mistake, since John was actually there.
Lastly in this chapter, the SAB notes that what Jesus tells Nathanael as a failed prophecy. I have to disagree with this assessment, of course. It could be that this prophecy was fulfilled and simply wasn't recorded by any of the four Gospels we have; Nathanael didn't write a Gospel. Much more likely, however, at least in my opinion, is that this is symbolic language, and Jesus is talking about some aspect of his ministry in which angels were involved in some way, and Jesus's incarnation in some way facilitated an opening of Heaven.