Wonderment,
If I may insert the following. I understand where you are coming from and this might help explain what is causing the difference in opinion here.
The Trinity Is Made of Three Entities...Yep, You Got It Right
First of all Trinitarians agree with you 100% that Jesus is NOT the same entity as the God he was "with" in John 1:1. Jesus is considered by Trinitarians to be an entity entirely separate and whole and different from God the Father, who is considered to be an entirely different Person, as they put it. These two separate Persons--completely individual and separate from the other--are also not the same entity as the Holy Spirit.
As the "one flesh" of humanity mentioned in Genesis consist of two entirely separate and individual entities, namely one husband and one wife, so the one God transcends this further by being made up of three entirely separate Persons, one Father, one Son, and one Holy Spirit…as they teach and believe. I am not here advocating this belief, mind you.
The problem is that you are taking this point as if it goes contrary to Trinitarian thinking or teaching, when in reality it does not. You are in total agreement with Trinitarians on this point. So nothing mentioned in Scripture that proves Jesus is not the Father is totally in agreement with Trinitarian doctrine. Trinitarians believe that Jesus is neither the Father, nor the Holy Spirit. Jehovah's Witnesses, who don't believe in the doctrine, often make the mistake that Trinitarians believe all three are the same Person, but such a view is incorrect as that would be considered heresy to believers in the Trinity.
With Your Lover, Not With Your Creation (That Is If You Were God...or the Flying Spaghetti Monster...or Elvis, even)
Also, in reality the word translated "with" doesn't mean exactly what we mean in English. It means "toward," and in fact is the same word used to describe a facet of "eros" that in itself leans toward "agape." It means to desire to be with as demonstrated by reaching out, to grasp in order to be practically one in substance.
This is a peculiar word since according to koine Greek rules about deities and spirituality, which the New Testament writers observed and used to their advantage many times, gods don't perform such an action among themselves.
It also goes contrary to the author's use of the expression "logos" or "Word" for Jesus. God's Word is that which "goes forth from" God. This is a Word that "moves toward" God, as if passionately in love or desperate to cling and merge with God. Regardless if we are Trinitarian or not, it is clear that the author is not using these terms literally. They are in fact the opposite of what one would expect to be used in reference to any deity, the Hebrew God especially.
The term appears again in Revelation to describe God being "with" humankind after the re-creation of the heavens and earth. While it would be perfectly fine to use this in reference to humans and their desire to be "with" God, it is odd to find the expression being used about a deity again.
Being that God does not live in a literal place like we do, God does not take up space—according to Trinitarian belief at least. Because of this one cannot literally be "with" God--and I know this is hard to understand—since God doesn't literally have a "side" to which we can be "alongside" him through. And the English word "with" gives us the idea of standing still in one spot next to God, but the word in Greek implies an incomplete action that is still occurring. Not the same thing at all.
So it's not literal. Nobody is literally with anybody else in these verses.
Sons are the Spitting Image of Their Fathers...But What's This About Spit?
Does the use of the word "Son" for Jesus mean that Christ is God's offspring? Nope. It does in English, but that is the secondary meaning in this instance of the word in Semitic usage.
In fact, we do have a saying borrowed from the Hebrews' use of the word "son": "He's the spitting image of his father."
What does "spitting image" mean? It comes from combing the words "spit and image." It means that a subject consists of both the stuff that its father is made of (the spit) and as a consequence acts and/or looks like their father (the image).
This explains Jesus reference to Judas as "the son of destruction" at John 17:12. Destruction is not a person who begot Judas. But Judas was acting as if he was made of the very same stuff as "destruction" was, that he was destruction itself!
You are likely familiar with the blind beggars who called out for Jesus to heal them and were hushed by the crowd. Why? Because they were blind beggars or poor? They were likely among the poor who were known to make up those crowds which hounded Jesus, so a class distinction was obviously not the issue.
No, the blind man (or men, according to one account), referred to Jesus as "Son of David." In other words, some of the first people to publically call Jesus of Nazareth "the Messiah" were these blind ones who wanted their sight. On this account the people hushed them.--Luke 18:39.
But they don't use the term "Messiah" at all, you say. Yes they do, they call Jesus "Son of David." Jesus was not the son of David, he was the son of Joseph. He was a great, great, great......grandson of David, but not a son. But like the term "son of destruction," the blind were indeed calling to mind the promise to David that his own seed would be the promised Messiah, and they were applying this to Jesus by calling him "Son of David" publically. That is why at Matthew 9:29 Jesus tells them to have their sight with the words: " Let it be done for you according to your faith." What faith? They had just publically put their standing in the synagogue on the line and named Jesus of Nazareth as the promised Messiah.
This is also why Jesus mocked the religious leaders as hypocrites because they kept using the phrase that they were "sons of those who murder the prophets." As stated in the NWT even: " Therefore YOU are bearing witness against yourselves that YOU are sons of those who murdered the prophets. Well, then, fill up the measure of YOUR forefathers" meaning "live up to what you are condemning yourselves as."--Matthew 23:32, italics added.
It is this usage of the Semitic "son" that gave Christians their first clue that Jesus was God Incarnate. Jesus never claimed to be a creation of God, much as an angel or man would or could. Jesus, on the contrary, acted and taught as the authority, not as one under authority. Because Jesus meant he was the equivalent of the perfect Adam when he called himself "Son of Man" (literally "son of Adam"), it was accepted that Jesus was also calling himself God in referring to himself as the "Son of God."
Now, this does not mean that I believe in the Trinity and claim that you should too. Nope, does nothing of the sort.
But I am showing you that the points you mention argue in favor of the Trinity, not against it.
Not 1 +1 +1 =1, But That 3 = 1 + 1 + 1
Trinitarians argue that God is made up of three distinct entities, just as 'one human flesh' is made up of the two distinct entities of wife and husband. The husband is not the wife, and the wife is not the husband, but the two are "one flesh" regardless.--Genesis 2:24.
Add to this that Jesus called himself the "Son of God," (and that English was not invented yet...English has only one meaning of "son," a male offspring of its parents, and no other meaning outside this), and since this is how his Christian audience came to understand it back then, they had no problem with later accepting the Trinity when it came down the line a couple hundred years later.
Yep, Jesus prayed to God, called God greater, etc., etc., but all this plays into Trinitarian thought, not against it like the Witnesses teach. The JWs teach the Trinity is three Gods in one, but Trinitarians believe in God in three Persons, a totally different concept. In their minds Christ is not equal to God, he is the Son of God, the spit and image, one and the same.
And that which is the same does not need to make itself equal to itself.
Finally, regardless if you believe in the Trinity or not or even accept the Flying Spaghetti Monster, it doesn't speak well of the NWT since it and the religion that developed it, never quite grasp the teaching they work so hard to preach against. You can't preach the Trinity wrong until you know what the Trinity is in the first place.
And all this is besides the true argument here, namely about translating in the "shadows," not regarding the validity of what may or may not be on the pages regarding Christ’s identity. Apparently the NWT itself isn't the only thing "in the dark" here. It appears the JWs and their religious leaders are in the dark about a great many things.