There is a problem with the Gospel of John. Firstly, John did not write it. Christians generously assume that John was “the inspiration.” You can take this how you want. It was thought by Eusabius
that John was written to counter various early heresies. This idea held sway until the late 19th century. Today, it is regarded as a composite piece constructed around 100AD by various authors from various sources (including their imagination) none of which are particularly reliable.
Examination of the Gospel shows that there are several authors. The first seems to have died part way into the work and his job was taken over by others who, like Eusabius, had their own agenda.
The Gospel of John developed over a period of time in various stages, summarized by Raymond E. Brown as follows:
1. An initial version based on personal experience of Jesus;
2. A structured literary creation by the evangelist which draws upon additional sources;
3. The final harmony that presently exists in the New Testament canon, around 85–90 AD.
Among others, Rudolf Bultmann suggested that the text of the gospel is partially out of order; for instance, chapter 6 should follow chapter 4:
4:53 So the father knew that it was at the same hour, in the which Jesus said unto him, Thy son liveth: and himself believed, and his whole house.
4:54 This is again the second miracle that Jesus did, when he was come out of Judaea into Galilee.
6:1 After these things Jesus went over the sea of Galilee, which is the sea of Tiberias.
6:2 And a great multitude followed him, because they saw his miracles which he did on them that were diseased.
Chapter 5 deals with a visit to Jerusalem, while chapter 7 opens with Jesus again in Galilee because "he would not walk in Jewry, because the Jews sought to kill him," a consequence of the incident in Jerusalem described in chapter 5. There are more proposed rearrangements
It does not end there. In http://textualcriticism.scienceontheweb.net/INT-EV/Jackson.html
What is remarkable in Jackson's work is that in spite of being very much a modernist and a realist about the internal evidence concerning John's Gospel, he nonetheless sees a clear break, a severe unconnectedness in John between 7:52 and 8:12 when the Pericope de Adultera is removed.
He is so convinced of this incontinuity, he uses it as evidence that John generally has suffered editing or dislocations by a final redactor or compiler. Although convinced by others that John 8:1-11 is an interpolation on textual grounds, he is just as certain that its removal solves nothing of the problem of John at this place in the text.
The Pool of Bethesda: John 5:3b-4
[Just] As certainly, the verses ch. v, 3 b, 4, are no part of the original Gospel, and here it is suggested that an evident gap has been filled in, by way of explanation, by some later hand; that, as the section originally stood, the genuine v, 7 was unintelligible, and hence the piece of information which, now properly relegated to the margin of the R.V., ultimately found its way into the text
At this stage, you may be coming to the conclusion that John is just so much garbage and invention that has been badly edited. However, it is little or no different from any of the other Gospels in this respect. Some of the scribblings bear a remarkable resemblance to the Qumran Scrolls and probably account for the “non-Jewish” nature of the Gospel.
So, when we come to ask what John:1:1 means, the answer is “God knows”. The additions, amendments, corrections, insertions, redactions, inventions, etc. etc. were done all over the place.
I looked up a commentary on John:1:1 and as a bonus got two. The first was an incomprehensible passage that simply assumed things. The second was a wall of text that left me feeing that nothing had been explained and that if so much writing were required to explain one verse, then the writer had no idea of what it meant either.