I remember two weeks after my conversion, my Sunday School teacher telling me the virgin birth couldn't possibly happen. If you're going to doubt the inspiration of God's word, this is the place to start for this is indeed one of the greatest miracle of all. Are you prepared to say that the virgin birth is a made up story or question the inspired story as told by God? You might as well chuck the whole thing out the window and become a Baal worshipper or something.
I can understand an agnostic or atheist not believing in God's inspired writings, but I sincerely don't understand how a professing Christian cannot understand the inspiration of God's word.
I suggest you read Codex Sinaiticus and tell me why are there two noncanonical books in it! Your claim that all the churches intrinsically read the same books is false, false and false. It's a myth!
The "Church" came to a consensus what books will be used. It was a decision of the hierarchs, plain and simple.
Eusebius, the first Church historian writes (c. 300 AD) about "disputed" writings (the Epistle of James, Jude and 2 Peter and 2 and 3 John!). Disputed in 300 AD?
The Church in Constantinople listed as "disputed" books the Shepherd of Hermes the Apokalypse of Peter and the Apocalpypse of John as late 9th century AD!
It was the Church in Rome of all places that disputed the book of Hebrews because it was not written by +Paul and therefore lacked the necessary apostolic authorship (which it does actually lack because the author is unknown!).
Today, we know that our Holy Bible has been corrupted by additions and deletions. Notable additions are Mark 16:9-20; Luke 22:19b-20,43-44; John 7:53-8:11 (the famous Pericope Adulterae) and 1 John 5:7b8a (the famous Comma Johanneuum).
I suggest you learn about the bible as much as you may have read from it. You may be surprised what the facts have to say.
To summarize: different Churches read different books, ignored other books, doubted some, etc. The only thing that is certain with respect to the NT canon before it was officially proclaimed at the end of the 4th century is that it was consistently inconsistent.