There is already a question on this site that addresses (1) whether the Word (i.e., the Son) is truly God, like the Father; and (2) whether Jesus Christ is fully God, and goes over the most important Scriptural passages to justify both claims. Have a look at What are the biblical arguments against Arianism? As that question makes clear, the questions you are asking were asked by the best minds of the Church right at the very beginning.
There are a number of important considerations here, not the least of which is how our salvation works. If Jesus is not God, then he does not have the power to save us: no mere man, however exalted, not even a mighty angel can do that. That is why the early Church Fathers—Alexander of Alexandria, Athanasius, Hilary of Poitiers, Ambrose, to name a few—were so concerned about Arianism.
(For the benefit of readers, Arius posited that the Son, or the Word, was not God, but in reality the first and greatest creature of the Father—a sort of super-angel. Arianism is the most extreme form of subordinationism, a fairly common current back in the third century. Arius did not, however, doubt the identification of Jesus with the Son.)
Against the large number of Biblical texts that support the divinity of the Word and of Jesus, there are a few passages that seem to contradict that idea.
Here are some ideas that might help in understanding the Church’s position:
“Word” can mean many things
One of the issues raised by the original poster is that the Word can refer to the Scriptures. Although this is true, it does not follow that this is the only meaning. Even in common parlance the words translated “word” (dabar in Hebrew, lógos in Greek) have a very wide variety of meaning: everything from literal “word” (like the ones that make up this sentence), to speech, to notion or concept, to rational order, to study. St. John when writing his gospel, was well aware that the Greek philosophers had made use of the term lógos in their philosophies.
It is clear, however, that St. John is giving the term a new meaning in John 1:1, when he says
In the beginning was the Word, and the Word was with God, and the Word was God.
The Greek grammar of this opening phrase does not permit any other interpretation except the full identification of the Word with God. And there can be no doubt that St. John, at least, affirms that this Word is Jesus:
And the Word became flesh and dwelt among us, and we have seen his glory, glory as of the only Son from the Father, full of grace and truth. (John 1:14).
(In the Old Testament, “glory”—shekinah—is an attribute of God alone.)
The Scriptures and the Son are given the same name, “Word,” because there is a similarity between them: the Son reveals the Father to us and makes Him intelligible, if you will. Likewise, the Scriptures contain those texts that God chose to reveal to man for his salvation.
Regarding certain passages of scripture
Let us now look at some of the passages suggested by the original poster.
The Father is greater than I
This is probably the most “devastating” passage is John 14:28:
You heard me say to you, “I am going away, and I will come to you.” If you loved me, you would have rejoiced, because I am going to the Father, for the Father is greater than I.
It would be easy to point to this passage to justify subordinationism—the idea that the Son is somehow inferior to the the Father—if it were not for other passages such as John 5:18.
This was why the Jews were seeking all the more to kill him, because not only was he breaking the Sabbath, but he was even calling God his own Father, making himself equal with God.
or John 10:30:
I and the Father are one.
or John 17:22;
The glory that you [Father] have given me I have given to them [the disciples], that they may be one even as we are one.
(Again, glory is an attribute of God alone, in the sense that John takes it. We can receive glory, in a way, but only God can give or communicate glory. Note that we disciples cannot possibly be one in exactly the same way as God is one—this is an example of Semitic exaggeration, to be taken in the same way as when Jesus says, “You therefore must be perfect, as your heavenly Father is perfect,” in Matthew 5:48.)
There are, therefore, essentially two ways to interpret John 14:28: (1) that when we consider Jesus in his current condition—incarnate “in the form of a slave” to use St. Paul’s words—then the Father is “greater” than Jesus because Jesus has voluntarily humiliated or emptied himself; or (2) that although by nature both the Father and the Son are perfectly equal, there is still a hierarchical order of origin—the Son has received everything He has, even His very Being, from the Father.
Which way did St. John intend? Probably both. John’s gospel is full of ambiguities that are intended to be taken in both ways.
No one is good except God alone
The passage in question is Mark 10:18 (and parallel passages), the episode of the Rich Young Man:
And Jesus said to him, “Why do you call me good? No one is good except God alone.”
We should note that taken perfectly ad litteram this is actually a false statement! There are plenty of good things: “And God saw everything that he had made, and behold, it was very good” (Genesis 1:31).
So Jesus must be saying something else; namely, that God is the the source of all goodness—indeed that He is Goodness Itself. Everything else derives its goodness from Him.
Looked at in this light, far from disproving Jesus’ divinity, this passage is an example of Jesus dropping a hint that He is God. The Rich Young Man intuited that Jesus was good to a degree greater than other Teachers, any with his question, “Why do you call me good?” Jesus hints at the reason why.
My God and your God
Then there is the passage from John 20:17:
Jesus said to her [Mary Magdalene], “Do not cling to me, for I have not yet ascended to the Father; but go to my brothers and say to them, ‘I am ascending to my Father and your Father, to my God and your God.’”
I think it is obvious that the first part of Jesus statement—to my Father and your Father—can easily be reconciled with Jesus’ divinity. He taught his disciples to call God “Father,” even though he was always very careful to distinguish the relationship between himself and the Father, the one between his disciples and the Father (as on this occasion). Jesus is, in the words of St. Paul, the “one mediator” between God and man, and so his relationship with the Father is special.
In reality, the only troubling expression is that Jesus calls the Father “my God.” However, it does not follow that Jesus is denying his divinity—indeed, he accepts the divine title only a few verses later in verse 28:
Thomas answered him, “My Lord and my God!”
(Note that “the Lord”—in Hebrew Adonai—was how the Israelites referred to God, in order not to pronounce the Holy Name, YHWH.)
Considering these passages, together with many others that positively indicate the divinity of Jesus, I think we can conclude that the fathers of the Council of Nicaea were correct, and fully scriptural, in proclaiming the full divinity of the Word; and the Council on Chalcedon was correct in proclaiming the full humanity and full divinity of Jesus.
