An excellent article at Parchment and Pen.

Is our Canon of Scripture a fallible collection of infallible books? To start at the beginning (definitions), the word "canon" means "rule" or "measuring rod". The Canon is the "rule" by which the church believes Scripture is measured. The Protestant, Roman Catholic and Orthodox churches all use different Canons - and the Orthodox churches even vary within that segment.

So the question is: How do we know what books belong in the Bible?

Roman Catholics and Orthodox will refer to the fourth century councils and Roman Catholics will refer to the Council of Trent, where Rome dogmatically defined the Canon is they define it today.

The author (C. Michael Patton) notes that every Bible has a list of books that is included in the Canon (whichever list they are using) - but that list is NOT part of the Canon. We have no infallible list of the Canon IN the Canon. So - since we (Protestants) believe that there is no infallible HUMAN authority - the only final and infallible authority is God and His Word, how do we know (infallibly) that we are reading the right books?

The short answer is that we can't. We cannot be infallibly sure (this side of the grave) that we have the correct list of books.

I didn't know that it was R.C.Sproul that first made the statement that we have a "fallible collection of infallible books". And then - what about interpretation? Are we left with a fallible interpretation of a fallible collection of infallible books? Is it time to migrate to the "one true church"?

Not so fast. In the end, this is an issue of epistemology. Epistemology deals with the question “How do you know?” How do we know the canon is correct? How do we know we have the right interpretation? Assumed within these questions is the idea of certainty. How do you know with certainty? Not only this, but how do you know with absolute certainty?

He answers:

1. This supposed need for absolute certainty is primarily the product of the enlightenment and a Cartesian epistemology. To say that we have to be infallibly certain about something before it can be believed and acted upon is setting the standard so high that only God Himself could attain to it. Outside of mathematics and analytical statements (e.g. a triangle had three sides), there is no absolute certainty, only relative certainty. This does not, however, give anyone an excuse or alleviate responsibility for belief in something.

I have some difficulty (as one of the commentors noted) that the supposed need for certainty came earlier than the enlightenment. However, the point remains that the lack of infallible certainty does not relieve us of the responsibility to believe and act upon the probability of certainty (see the article for examples).

2. The smoke screen of epistemological certainty that seems to be provided by having a living infallible authority (Magisterium) disappears when we realize that we all start with fallibility. No one would claim personal infallibility.

Therefore it is possible for all of us to be wrong. We all have to start with personal fallible engagement in any issue. Therefore, any belief in an infallible living authority could be wrong. As Geisler and MacKenzie put it,

As the author puts it, same river, different boats.  I have a fallible faith in God to preserve His Word.  Another person may have a fallible faith in a church to preserve God's Word.  Either way, we both start with our own personal fallibility.

Is there a place for doubt?  Here's a post. I like this paragraph:

Existential doubt also plays other roles too. It serves to temper an unhealthy certainty that one may have about her direction in life, her agenda, or certain courses of action. It serves to make the Christian aware of the fact that she walks by faith, and not by sight. It serves to remind her that she is wholly dependent upon God’s provision. It also impels her to seek out her brothers and sisters for comfort and encouragement, although sometimes out of fear of rejection or condemnation, she may not do so.

Are we shown doubt in the Bible?  One of my favorite verses:

Mark 9:23-24. And Jesus said to him, “‘If you can’! All things are possible for one who believes.”  Immediately the father of the child cried out and said, “I believe; help my unbelief!”

The father believed, and yet knew that somewhere, he harbored doubt.  And he asked Christ to help (and Christ did).

Yes, there is a place for doubt.

Without doubt, we are sure.  With surety, it is not faith.

Hebrews 11:1 Now faith is the assurance of things hoped for, the conviction of things not seen.

Romans 8:24 For in this hope we were saved.  Now hope that is seen is not hope.  For who hopes for what he sees?

If there is no room for doubt, it is not hope, and it is not faith.

That applies to the Canon as well.  Do I have an infallible assurance of the "right" Canon?  No, but I do have a historical list that includes the books that my Bible include.  I have historical evidence that the Hebrew Jews did not include the parts that my Bible does not include.  I have historical writings that tell me that (world wide), there is room for doubt, but also room for hope and faith that my Bible includes what it needs to include to lead me to eternal life and to a life of Christian faith and conduct.

Is there more?  Some have a fallible faith in a worldly authority that calls itself infallible.  Do I have that same fallible faith in that same authority? No.  For now, I walk by faith, not by sight.