15) If the books of the New Testament are “self-authenticating” through the ministry of the Holy Spirit to each individual, then why was there confusion in the early Church over which books were inspired, with some books being rejected by the majority?

The Question's premises are unproven, we don't know if everyone in attendance was an Elect of God.

History reveals there was a flood of spurious revelation which is what made the scope of the canon an issue. It follows this flood was a satanic plot to confuse the Word of God with his word, therefore it is likely he had his plants sown among the wheat:

Matthew 13:39 The enemy that sowed them is the devil;

The confusion may have been his work.

However, its all speculation, too little of the event is known.

We do know 66 books were always received as Scripture, somewhere in the church. That proves God always authenticated His Word and still does so today.

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The times of this ignorance God winked at; but now commandeth all men every where to repent:

Behold, I stand at the door, and knock: if any man hear my voice, and open the door, I will come in to him, and will sup with him, and he with me.-kjv