The Bible interprets itself. It does not rely on linguistic, historic, anthropological, theological and ecclesiastical authorities. In fact, the theological and ecclesiastical authorities in particular have made the book all but incomprehensible. They are the ones who use words like incarnation, trinity, same substance, and other words that are actually not found in the Bible. They must be read into it, i.e. eisegisis.
As far as unity vs. uniformity is concerned, God is not dependent on a committee. He does not rely on our agreeing who and what He is. God tells us who and what He is in the Bible. All we need to do is read it and believe it or not.
Reading John 1:1 and indiscriminately substituting the word "Jesus" for the word "word (logos)" is the epitome of eisegesis. Why not see how the Bible uses the word logos? That would be exegesis, which as you pointed out is the true method. Let the Bible speak for itself.
The word logos is a rich word that is difficult to translate into English by one word. It means the thoughts in the person who speaks the words. It tells us what is in the mind of the speaker. It can be thought of as what God had in mind in the beginning. It was his plan.
Jesus did become the logos, that is true. But he became the logos, not in the beginning, but when he was born. The logos, not Jesus, was literately with God in the beginning. Hebrews 1:1-2 fits perfectly with that idea.
Heb 1:1-2,
1 God, who at sundry times and in divers manners spake in time past unto the fathers by the prophets,
2 Hath in these last days spoken unto us by [his] Son, whom he hath appointed heir of all things, by whom also he made the worlds;
In the past God spoke by the prophets, the law, and a few other ways. That is how he made his logos known to man. But as verse 2 says, at some point Jesus was born and he was a perfect image of God. Without fail, the man Jesus always spoke God's will to the letter. His actions were a perfect representation of God. It is in that sense that the logos became flesh.
You may look at the last phrase in Heb 2:2, "by whom also he made the worlds" and say Jesus created the universe and was thus God. That is because by the time English Bibles were written the trinity had been an established doctrine and the translators made liberal use of eisegesis.
The word "worlds" is the Greek word "aeon" and it should be translated as "ages" as in the age of Eden, the age of law, the age of grace, or the coming age of the new heavens and new earth. We've had several different ages but they were all built around the Lord Jesus Christ. Hebrew 2:2 is simply telling us that Jesus was the key player in God's plan or logos and that is absolutely true, but none of it makes Jesus God. There is one God, and unlike many of the pagan gods, he is not three gods in one. He is simply one.