What key changes does the main character(Toby/Jack) go through over the course of the novel?
Some of the major changes that Cory go through are the loss of some of his innocence as he sees some of the hard things that his father must handle and some of the ways that things aren't as happy as they seem everywhere. He learns that he cannot depend on his own insight all the time and must work hard and be willing to learn from others to gain a place in the world and to overcome hardships.
As an example, he worries about Cory pretty often, since he is so soft spoken and doesn't seem to know how to take care of himself. Of course once Cory demonstrates all the skills he learned by working super hard on them over the summer to defeat the Branlins, Cory understands that he too can accomplish something like that, given that he works hard enough to accomplish it.