Maybe the inability to see the work of the Holy Spirit and to insist that the Canon was put together hundreds of years after the fact is at the root of your doubts about Christianity. I suppose I would look at it the same way if I thought a bunch of guys put everything together.
Claiming that it was the work of the HS is a conjecture which in and of itself cannot be proven. Looking at the lack of uniformity and the variety of other books which were included in individual early church canons and lists of various Christian apologetics, it is oblivious that such a conjecture is patently false,unless of course we are willing to admit that there was either more than one "Holy Spirit" at work or that one Holy Spirit created many different "works".
As late as the middle of the 4th century, preserved codices of Christian books contain scrolls that are now considered profane (Epistle of Barnabas, Shepherd of Hermas, etc.). How can that be if this was the work of the HS?
The fact that most of the books of the NT were shared by most churches and apologetics does not in and of itself show the whole picture: the individual canons contained books that, somehow, the HS or whoever later decided were not fit for inclusion.
And, I have no doubts about Christianity. I merely see the less romantic view of it.