Take them for what they are: those annoying questions at the back of the book that teachers in school force you to answer in the form of an essay. But, you have to admit--begrudgingly perhaps--they do make you think. And thinking's good! Excellent for reading group discussions, that sort of thing.
Jake is clearly an imaginative protagonist. How much of his experience do you think is a product of his imagination and how much is really happening?
Who is the Melting Man? What does he want? Is his domain within the ancient tree real or a part of Jake's imagination?
What is the role of television in The New Flesh? What does the television set symbolize?
How is Jake's family's history important to the novel? How much to you think Jake's grandfather knows? Where do you think Jake is going at the conclusion of the novel?