You are making a generalized statement based on the canons of several fathers. It took four centuries for the whole Church to accept (at leats in the west) +Athanasius' canon. Even after that, the East did not use the Apokalypse of John for another 400 years.
Yes, the core was agreed upon very early. There was almost no disagreement (save for the likes of Marcion and Valentius), on the Gospels and the Epistles. But these four examples I listed are by no means the only canons that existed. You mentioned the Muratonian Fragment, and there are at least half a dozen others, all agreeing on the core.
You mention the Protoevangelium of James. The Church never "eliminated" it from the readings; it just never elevated it to the dignity of scripture because it was written in the middle of the 2nd century and is therefore not of apostolic origin!
But there are no known objections to the Protoevangelium being read and used in the Church. No one objected to its content.
The Church took it as true although not scriptural. It is a historical account that also reflects the belief of the Church at that time, namely that the Blessed Theotokos remained a virgin after the Birth of her Son, just as she remained a virgin at His conception.
No one questioned it. It was what the Church believed then and it is what the Church believes now. A writing can be true without being inspired.
It was done with no printing presses, computers, fax machines, or system of communication other than letter or face to face conversation
Anything that was believed to be of apostolic origin was automatically accepted as significant. They were read in churches as such. Those that were "questionable" were deemed such because their apostolic origin could not be established.
However, +Justin Martyr, as late as 150 AD, refers to them as "apostolic memoirs" and not as scriptures.
One hundred years without computers and Internet is still enough time for a handful of books to find favor in a like-minded community. Nothing really magical about it that necessitates divine intervention.
No authoritative councils as you mention, because the majority of bishops were in agreement. They were all either directly ordained by apostles who walked with Christ or they were ordained by someone who was ordained by an apostle. There was no reason to deviate to any large extent. The Church was struggling against persecutions and there was little time for theological disagreements.
But there were deviations as evidenced by epistles of +Ignatius (c 130 AD) and +Irenaeus (c 180 AD), and there were such individuals as Marcion and Valentius, and Origen and Tertullian who shortly thereafter began to slip into heresy. And when the various ideas about Christ's own nature(s) began to crop up, it was obvious that the scriptures were being misinterpreted by many.
This necessitated the first councils...the issues regarding the very core of Christian beliefs: the Holy Trinity and the Duality of Christ. And it was over these issues that the first schism occurred. Not over Mariology and her perpetual virginity found in the Protoevnagelium, or over the Apocrypha, or the Septuagint, but over the the nature of the Godhead and Christ.
I don't see the Holy Spirit creating division and disunity in the Church, and there was plenty of that from the very beginning. The "miracle" of the scriptures being agreed upon is based on the simple belief that they are of the apostolic origin (such as Hebrews, 1 and 2 Peter, 1,2,3 John, etc.) even if they were later ony attributed to an apostle.
“This necessitated the first councils...the issues regarding the very core of Christian beliefs: the Holy Trinity and the Duality of Christ. And it was over these issues that the first schism occurred. Not over Mariology and her perpetual virginity found in the Protoevnagelium, or over the Apocrypha, or the Septuagint, but over the the nature of the Godhead and Christ.”
This is really an excellent point and as someone with a devotion to Panagia I never really thought about it but its demonstrably true. During the first 1000 years of The Church, there simply wasn’t any question about the Theotokos or her perpetual virginity or her dormition and the facts surrounding it or her childhood, the Annunciation, etc. as there certainly were questions on the nature of the Trinity and of Christ and later of the veneration of icons which necessitated Eumenical Councils. But no questions, no heresies, about the Theotokos. Interestingly, there are comments made in the 7th century work “The Spiritual Meadow” about the devotion of a certain heretical sect, the Severians, which had been around for sometime by then, to the Theotokos. It seems even a major heretical group had no problems with the Marian beliefs of The Church.
Origen was very quick to point out it's recent appearance and questionable details.
The Church took it as true although not scriptural. It is a historical account that also reflects the belief of the Church at that time, namely that the Blessed Theotokos remained a virgin after the Birth of her Son, just as she remained a virgin at His conception.
Which Church?
Origen noted that "while the notion might seem pious, it was not unlikely that the obvious interpretation of Scripture (that Mary bore them for Joseph) was true and acceptable" when talking about the brothers of Jesus.
It is eye opening how that forgery followed so shortly after the forgery "the Acts of Paul and Thekla". In this case it was Tertullian who quickly noted it being a forgery. What makes it all so interesting is Thekla is written about at length. Her praise of virginity. She was a devoted disciple. Her aggressive evangelism and refusal to be "pushed around" by men. Tertulian complains some Christians were using Thekla as an example to legitimate women's roles of teaching and baptizing in the church.
It's a good thing that those of the other school of thought had an example of a submissive, quiet woman content to sit in the background, Mary. The shame of it is in both cases the books were forgeries.