Some critics of the fourth gospel suggest chapters five and six are transposed and thus out of sequence; in other words, Chapter six should precede chapter five. Benjamin Bacon advocated this approach in the early 1900s, although he would later reverse this position. He suggests the Apostle John had sources outside the other three gospels. Like other scholars, Bacon believed the Apostle John did not write the prologue, which someone else wrote these verses when the gospel was rewritten after the death of John. Bacon advocates a pre-Galilean ministry, which necessitates a reorganization of the first four chapters, resulting in a more extensive period in Galilee. This makes this portion of the gospel more similar to Mark. Like others, he advocates switching chapters five and six. “With 5:1 following chapter six, the post-Galilean ministry of the original gospel begins. It spans a year and substitutes a series of festal visits (chapters 5, 7-12) of Jesus to Jerusalem.” 
It is true that if one looks at the start and end of chapters four, five, six, and seven, the concept does have some validity. “If we reverse the order of chapters five and six, and put 7:15-24 after 5:47, the two moves lend support to one another, and we arrive at the simple result: that chapter four was followed at once by chapter six, and that after this climax and turning point in Galilee, the reader learns of the equally dramatic but even more menacing developments of Jerusalem. Chapter five continued by 7:15-24, tells of the event that started the clash, a healing on the Sabbath, then of a revelation discourse, or a decisive nature, followed by a controversy on fundamentals.”  Keener notes that “while such transposition is conceivable for pages in a codex, it is difficult to conceive such an accident for the earlier versions, on scrolls; and no manuscripts attest the alleged transposition.” 
Haenchen explains the problem could be because the “fourth gospel was written on individual sheets, which were then later combined into a scroll. The joins came loose in the course of time and some sheets were reinserted at the wrong places.”  Ashton reaches the same conclusion as Keener, but, like Haenchen maintains the gospel was written not on a scroll but codex and notes that “if one is relying on the dislocation hypothesis it is too good to be true. For if the Gospel had in fact been composed not on a scroll, but a codex and its leaves had somehow become lost and jumbled up in the way the theory requires, then it becomes impossible to believe that once they had been gathered together again the evangelist (or anyone else already acquainted with the material) would have reassembled them in the wrong order.” 
Another problem with reorganizing the Gospel, so the ministry of Jesus was in Galilee first, and Judea second is that it results in Jesus and His disciples not going to Jerusalem for any of the feasts, as the current order records. Judaic Law mandated that anyone living within a certain distance of the Temple must attend the major feasts. Jesus, in Galilee, was under no obligation to attend, but He apparently, according to John, chose to travel to Jerusalem via Samaria to celebrate the feasts. His encounter with the woman at the Sychar well and the refusal of the village in Samaria to provide Jesus and His disciples lodging on one of their later trips show He customarily took the direct route instead of crossing to the Transjordan and passing around Samaria before turning west back to Galilee.
It is pertinent to note that the Apostle John uses the expression “After these things…” to mark a transition. There is no clue as to the period to which the phrase refers, which is likely intentional. It could have been mere days or a period of several months. John tells of the Christ and why his hearers/readers should believe in Jesus rather than narrating a chronology of His activities or writing a biography. “If one focuses, therefore, chiefly on the lack of a proper transition between chapters five and six, it cannot be denied that the hypothesis of their reversal has some appeal. One may question, however, to what degree the evangelist felt it necessary to give the reader detailed insight into the chronological sequence of the events narrated; it is clear that the kerygmatic content of these events was of more importance to him.”  Others point out a problem between chapters six and seven. At the chapter break, the sudden shift from Judea to Galilee presents a difficulty because Jesus was presumably already in Galilee. The is one of the arguments for placing chapter six before chapter seven, but this suggestion causes other problems in the narrative.
While we are talking about this portion of the gospel, it is necessary to clarify another point. Many scholars question the validity of the first eleven verses of chapter eight telling of the confrontation between Jesus and the woman caught in adultery. These verses are “lacking in the papyri, the oldest uncials, and in the test of the Eastern Fathers. The periscope into the gospel of John at various points and event after Luke 21:38.”  Thus these verses were likely not part of the original manuscript.
Another point of confusion refers to the signs of Jesus. The first sign of the Fourth Gospel is His turning water into wine at the wedding in Cana. The gospel makes the observation that He worked signs in Jerusalem, presumably the signs of which Nicodemus spoke when he came to Jesus at night. However, John identifies the miracle of healing the nobleman’s son as the second sign. To some, this is cause for concern because of the lack of specificity in the narrative. Despite the fact that a scholar such as Brown suggests a possible problem, the simple explanation is that the events John chose to designate as signs were instances revealing a new facet of the divinity of Jesus. The first sign is unique in that He showed His authority over quantity. The second sign is unique in that He healed at a distance. He could have healed any number of people suffering from various ailments while He was in Jerusalem, but, because they did not reveal new information about Jesus, the Apostle John chose not to tell of these signs.
Kysar writes that the structure of the fourth gospel is such that the chapter sequence is, in fact,
correct. The gospel breaks between chapters eleven and thirteen with chapter twelve serving as a bridge. In the first half of the gospel, chapter six is the fulcrum where the opponents of Jesus begin to plot against Him. In the second half of the gospel (chapters thirteen through twenty-one), chapter eighteen serves as the fulcrum in that it picks up the theme from chapter six in the plot against Jesus that had been absent in chapters thirteen through seventeen. He suggests the fourth gospel contains “a distinctive rhythm. The author narrates, first, a public ministry of Jesus; second, a private teaching of His disciples; third, a public trial and execution; and finally, a series of private appearances to His disciples. The rhythm between the public and private work of Jesus is the cadence of the narrative.”  According to Kysar, the fourth gospel can be mapped as a sequence of dramatic up and down actions resembling the letter “W.” The prologue (1:1-18) starts on a high peak and concludes on a low plane. The drama builds with signs and discourses (2:1-5:47) and continues until chapter six, which is a high point, the opposition beginning to form against Jesus. The reference in 6:31 to Judas, who would later betray Him, highlights this opposition. The narrative trends downward with the private teachings and discourse of Jesus to the disciples. This period reaches its lowest point when Jesus announced the hour had come (7:1-12:23). The narrative begins an upward trend and peaks with the trial, execution, and burial of Jesus (12:24- 19:42). The narrative makes a dramatic downward movement in the narrative with the burial of Jesus. An equally strong upward movement starts in 20:1 with the resurrection and private meetings with the disciples that conclude in 21:25.