Can you tell me why there are so many books talked about in the Bible that are not part of the Bible? Here is a list of them: book of the wars of the Lord (Num 21:14), book of Jasher (Josh 10:13, 2 Sam 1:18), book of the acts of Solomon (1 Kings 11:41),† book of Samuel the seer (1 Chr 29:29), book of Nathan the prophet (1 Chr 29:29,†2 Chr 9:29), prophecy of Ahijah (2 Chr 9:29), visions of iddo the seer (2 Chr 9:29, 12:15, 13:22 ), book of Shemaiah (2 Chr 12:15), book of Jehu (2 Chr 20:34 ), sayings of the seers (2 Chr 33:19).
How about the earlier Epistle of Paul to the Corinthians (1 Cor 5:9) †or the one to the Ephesians (Eph 3:3) or the epistle to the Church at Laodicea (Col 4:16) Maybe the plan for salvation was in one of these. Could this mean that the Bible is not complete? Could some truth not be in the Bible as we know it? Should we trust the men that held the Council of Nicea? Was the closing of the canon of Scripture by divine decree? Was the Lord done talking and teaching us?† Could you tell me what Peter meant when he said the heavens must receive Jesus "until the times of restitution of all things" (Acts 3:20-21)? Did he mean that the gospel of Jesus Christ would need to be restored?
A list of possible external books already exists on this web site in the Topical Index, under "Bible." As discussed in an earlier question, "What is the Book of Jashar?" the fact that the Bible refers to other books does not necessarily imply that the other books were inspired. And quoting from the books doesn't necessarily means the quote was inspired of God. It just means that the author of the book had said something that the inspired writer found useful in illustrating his point.
I suspect a few of the books are actually in our Bibles, but we know of them by a different name. The letter to the church at Laodicea is a good example of this. See "The Letter to Laodicea" for details. I suspect some of the references in the Old Testament refer to portions of the composite writings, such as I Samuel, II Samuel, I Kings, II Kings, I Chronicles and II Chronicles, refer to the author of that section though we no longer know who wrote which sections.
"How that by revelation He made known to me the mystery (as I have briefly written already, by which, when you read, you may understand my knowledge in the mystery of Christ)" (Ephesians 3:3-4).
Paul is referring to what he already written in the first two chapters of Ephesians. Even if you wish to argue that he is referring to a separate document, he does not state it was another letter to the Ephesians, only that it was something he wrote already. Letters were circulated by the churches as they were being written (Colossians 4:16).
"I wrote to you in my epistle not to keep company with sexually immoral people" (I Corinthians 5:9).
Once again, it is not a necessary conclusion that Paul is referring to a different, earlier letter. It can simply be a reference back to what he has already penned in this epistle (the first part of chapter 5). Similar wording (in the Greek) is found in I Thessalonians 5:27 and II Thessalonians 3:3-4, which are clearly self-references to the same letter in which they appear.
Since God stated, "All Scripture is given by inspiration of God, and is profitable for doctrine, for reproof, for correction, for instruction in righteousness, that the man of God may be complete, thoroughly equipped for every good work" (II Timothy 3:17), and "as His divine power has given to us all things that pertain to life and godliness, through the knowledge of Him who called us by glory and virtue" (II Peter 1:3), there is no reason to suppose that we do not know of God's plan for the salvation of mankind through the Bible -- quite the opposite actually.
As Jude stated, "Beloved, while I was very diligent to write to you concerning our common salvation, I found it necessary to write to you exhorting you to contend earnestly for the faith which was once for all delivered to the saints" (Jude 3). Our salvation was delivered once, for all people for all times. Jude makes it clear that there would not be further revelations, so yes, the closing was by Divine decree several centuries before various councils met.
"Repent therefore and be converted, that your sins may be blotted out, so that times of refreshing may come from the presence of the Lord, and that He may send Jesus Christ, who was preached to you before, whom heaven must receive until the times of restoration of all things, which God has spoken by the mouth of all His holy prophets since the world began. For Moses truly said to the fathers, 'The LORD your God will raise up for you a Prophet like me from your brethren. Him you shall hear in all things, whatever He says to you. And it shall be that every soul who will not hear that Prophet shall be utterly destroyed from among the people.' Yes, and all the prophets, from Samuel and those who follow, as many as have spoken, have also foretold these days" (Acts 3:19-24).
Since Peter's emphasis is on listening and obeying the teachings of Christ that were given to these people, the time of restoration of all things does not imply that the gospel itself would need to be restored. Such a reading would not even match Mormon doctrine since the statement is that Jesus would return when it was time for the restoration of all things. Since Mormons do not believe the return has happened yet, it follows that the restoration of all things has not happened yet.
The "all things" is not everything in general, but the phrase is qualified. It is "all things, which God has spoken by the mouths of all His holy prophets since the world began." It refers to a healing or a restoration between man and God that all the prophets have talked about, such as in Isaiah 59:1-2. Peter states that this will come about when people repent of their sins and are converted to the gospel, "so that times of refreshing may come from the presence of the Lord, and that He may send Jesus Christ." The "times of refreshing" and the "restoration of all things" refers to the same thing and lead to the same event -- the return of Jesus Christ. At that time the breach between man and God, caused by sin, will be healed (Romans 8:22; I Corinthians 15:28).
Finally, the councils did not decide what books should or should be in our Bibles. It recognized the books that have always been accepted as the inspired words of God. See: "How did your Bible come into existence?" and "How did the correct books get added to the Bible?" for details.