John 1:1-14 is a narrative about the how God manifested a human from His word (a word, speech, or divine utterance.) The word is personified, but a word isn't an actual person. John 1:10 states that He was in the world but the world did not know him. This isn't about Jesus since the New Testament teaches that Jesus came down from heaven. The one in the world was the Father as the OT states. God, the True Light, gives light to people entering the world. When Jesus entered the world God gave light to him.
1 Timothy 3:14 doesn't mean God manifested as a human. It means that he manifested a human. A human God creates to many sin issues like idolatry. That isn't something God would do because God does not tempt anyone to sin according to James 1:13.
Isaiah 7:14 is about a human. The next verse says Immanuel needed time to reject evil and choose good. That isn't a characteristic of God.
God is with us means just that, but it doesn't mean Jesus is the actual God with us. Immanuel is just a name with that definition. God was with Jesus and in effect also with those with whom Jesus was with in the way Acts 10:38 says:
38how God anointed Jesus of Nazareth with the Holy Spirit and with power, and how Jesus went around doing good and healing all who were oppressed by the devil,
because God was with Him.
At Jesus' water baptism there were not three present. I think you are projecting that assumption into the Bible because you still think there is a Trinity Godhead. What happened at the water baptism was God anointed Jesus with the Holy Spirit and this enabled God to use him for healings.
The Word cannot be a "personification", the context says the Word became flesh and John bore witness of HIM, and then the Word is identified as Jesus Christ through whom grace and truth came:
14
And the Word became flesh and dwelt among us, and we beheld His glory, the glory as of the only begotten of the Father, full of grace and truth.
15
John bore witness of Him and cried out, saying, "This was He of whom I said,`He who comes after me is preferred before me, for He was before me.'"
16 And of His fullness we have all received, and grace for grace.
17 For the law was given through Moses, but
grace and truth came through Jesus Christ. (Jn. 1:14-17 NKJ)
Personifications aren't born a few months after John the Baptist, nor did we receive grace and truth through a personification, because such things are poetic fiction and not real human flesh like Jesus Christ.
As for 1 Timothy 3:16, text plainly states God was manifested in the flesh:
16 And without controversy great is the mystery of godliness:
God was manifested in the flesh, Justified in the Spirit, Seen by angels, Preached among the Gentiles, Believed on in the world, Received up in glory. (1 Tim. 3:16-4:1 NKJ)
Jesus was "preached among the Gentiles and believed on in the world," not a personification or nameless human.
Christ's words "they shall all be taught by God" proves what Christ thought of Himself, as He taught them:
43 Jesus therefore answered and said to them, "Do not murmur among yourselves.
44 "No one can come to Me unless the Father who sent Me draws him; and I will raise him up at the last day.
45 "It is written in the prophets,`
And they shall all be taught by God.' Therefore everyone who has heard and learned from the Father comes to Me. (Jn. 6:43-45 NKJ)
The prophets didn't prophesy a "personification" would rise from their brethren like Moses:
"The LORD your God will raise up for you a Prophet like me from your midst, from your brethren. Him you shall hear, (Deut. 18:15 NKJ)
Its absurd to read " "The LORD your God will raise up for you a Personification like me from your midst...."
A Prophet like Moses cannot be a personification that exists in in poetic literature.
Nor do virgins conceive personifications, and a poetic personification wouldn't be a sign to anyone:
"Therefore the Lord Himself will give you a sign: Behold, the virgin shall conceive and bear a Son, and shall call His name Immanuel. (Isa. 7:14 NKJ)
Of course God was always with Jesus. Its absurd use of language to say God was with a "personification"!
Three were present at Jesus' Baptism, the Father speaks CALLING JESUS His Son, not a personification; the Holy Spirit is as a Dove rests upon Jesus, and this isn't a poetic story in a fairy tale, it actually happened to Jesus; John the Baptist couldn't baptize a personification in the Jordan River:
9 It came to pass in those days that Jesus came from Nazareth of Galilee, and was baptized by John in the Jordan.
10 And immediately, coming up from the water, He saw the heavens parting and the Spirit descending upon Him like a dove.
11 Then a voice came from heaven, "You are My beloved Son, in whom I am well pleased." (Mk. 1:9-11 NKJ)
The Father wouldn't be pleased by a mere personification.
But a man running from scripture, its plain obvious meaning, could be a personification of a fool.