I believe that John 1:1 has as a parallel passage Ephesians 4:10.
God descended to become a Man, out of eternity into time, then ascended back out of time into eternity, to fill all things (and also transcended created time once again).
The pre-incarnate Christ (the Father) exists outside of time. The incarnate Christ (the Son) is a finite human being (while also being fully the Lord God; the Father incarnate...Isaiah 9:6) and bound to time. The after-incarnate Christ (the Holy Ghost) ascended to again be outside of time (Ephesians 4:10, Luke 23:46; see also 1 John 4:1-3, 2 John 1:7) and therefore exists as a distinct individual dwelling in eternity, outside of time. But the same Person as the Father (the eternal Spirit, John 4:23-24), yet distinct from the pre-incarnate Christ. The Holy Ghost also descends as often as He wills to come and dwell in believers; and He is the Person of the Trinity who does dwell in believers (2 Timothy 1:14). Yet, because He is in a sense the same Person as the Father and the Son (while also being distinct from the other Two), it can be said that the Father (Ephesians 4:6) and the Son (Colossians 1:27) also dwell in every believer. Yet the Bible teaches that there is one Spirit (Ephesians 4:4) and that God (the Father) is that Spirit (John 4:23-24). There is one Lord (Ephesians 4:5, 1 Corinthians 8:6) and God (the Father) is that Lord (Matthew 11:25, Luke 10:21; Acts of the Apostles 4:24, Mark 12:29 (kjv)). Yet no one can say that Jesus Christ of Nazareth is the Lord except by the Holy Ghost (1 Corinthians 12:3, Acts of the Apostles 4:10-12).
Thus, in John 1:1: In the beginning was the Word, and the Word was with God, and the Word was God.
Now the Word that was with God, in this scenario, would be the Father (for He was God); and the Word that was God (who was also with God); would be the Holy Ghost. The pre-incarnate Father is the One who became flesh. The Holy Ghost (the after-incarnate Father) did not have to become flesh because He had already been flesh.
Now when the pre-incarnate Father descends to become a Man, He is given the title Holy Ghost so that we may know that it is speaking of the same Person (in Luke 1:35). But truly it is the pre-incarnate Father who descends.
Now some may think that I am denying the Trinity in all of these statements. But I don't think that I am. I am attempting to refute Tritheism; which some people mistake the idea of the Trinity to actually mean.
And I am not promoting the concept of modalism either. Because while the Spirit inside of the human Jesus is the same Person as the Father (John 14:7-11), the human Jesus is not the Father in that the pre-incarnate Father's existence is outside of time: He inhabits eternity with him who is of a contrite and humble spirit (Isaiah 57:15). He is transcendent, Omnipresent, and in all and through all. The Father in the Son, on the other hand (being the same Person/God as the eternal Spirit, who is the Father, John 4:23-24, Ephesians 4:4) inhabits the human body of Jesus Christ: He is a finite human being in His humanity (1 John 4:1-3, 2 John 1:7)...and therefore the Father, Son, and Holy Ghost, in my view, are distinct from each other, who each contain a consciousness of their own.
We must remember that God is one Spirit (John 4:23-24, Ephesians 4:4).
And Jesus, being God, is that Spirit (John 4:24) although He inhabits the human body of the Son, which is made of flesh (again, 1 John 4:1-3, 2 John 1:7).
All of this is to defend the common definition of the word "One" in Deuteronomy 6:4; while the idea of a compound unity is not completely denied by the statements above.
Finally, I want to make note of the fact of what it says in Ephesians 3:11. If you think on what this verse might mean in light of what I have spoken, you can gain insight into what I am saying.
Love in Christ,
justbyfaith