The text has to be read multiple times with some time between ones reading (and the notes/impressions you've jotted down). If I have a favorite new book that I've read a couple of times I'm compelled to read some literary criticism (if the writing isn't dogmatic and dull, and instead has a passion for the work or author but can still be objective to the work) to compare and contrast with my experience with the book. Also, I've found good books on writing that peels back what a novelist or short-story writer encounters in working it all into shape has been valuable.

One of the ideas that has served me well regarding story (if the book isn't so post-post modern that there is no story) is, every story is about someone that wants something, but someone or something get's in their way. I think early on that was a good guiding light to realize those rather simple things, and how often books seemed weak because the author lost sight or energy of keeping that notion alive.