In my opinion Canon Revisited by Michael Kruger is a landmark work on the New Testament canon. It's not a book-by-book analysis, but a treatise on canonical method. Kruger masterfully defines and defends the self-authenticating model, in contrast with the community-determined and the historically-determined models.
Here's a highlight, from "The Divine Qualities of the Canon", on why we should be careful not to link the NT canon to current critical assessments of the New Testament...
It is here, then, that we come to the crux of the matter. Should Christians abandon their commitment to the canon’s authority because biblical critics, who view scriptural interpretation as merely a human enterprise, claim to have discovered theological incongruities? No, because Christians have no grounds for thinking that those without the Spirit can rightly discern such things—indeed, Christians have good grounds for thinking they cannot. One might as well ask whether Joshua Bell, world-renowned violinist, should abandon his musical career because his concert in a Washington, DC metro station (on a 3.5-million-dollar Stradivarius) was met with disinterest and boredom.* The answer depends on whether we have reason to think that the average pedestrians in the DC metro station can identify musical genius when they hear it. Apparently they cannot. When all was done, Bell had not drawn a crowd, was never given a single instance of applause, and left with a paltry $32.17.
At this point, the critic of the New Testament might respond by saying that this whole affair sounds suspiciously circular. After all, it is no surprise that Christians “conclude” that the New Testament is harmonious— they already believe in the truth of the New Testament from the outset! Therefore, it is not proper (it is argued) to allow those who believe the New Testament to be the final judges of its theological harmony. However, this argument cuts both ways. If the Christian assumes the truth of the New Testament while arguing for its unity, then it is clear that the non-Christian assumes the falsity of the New Testament while arguing for its disunity. He assumes that (at least) 1 Corinthians 2:14 is mistaken and that New Testament theology can be understood rightly by those without the Spirit. Thus, one could ask why we should allow those who have already rejected the New Testament to be the final judges of its theological harmony? Again, keeping with the music analogy, that would be like allowing a person who is tone-deaf (and thus rejects this whole concept of being “on key”) to judge a singing contest. If the tone-deaf person were kept from judging, he might object and claim that this whole “on key” thing is a sham run by musical insiders who claim to have a special ability to hear such things. But despite all the protests, the truth of the matter would remain: there is such a thing as being on key whether the tone-deaf person hears it or not.
*For this true story, see Gene Weingarten, “Pearls Before Breakfast,” Washington Post, April 8, 2007.