Yep, we plan to! And if you don't mind waiting, I'd probably recommend holding off until we've made all the changes we're going to make to the console version(s) – which we're bringing back to the desktop versions, of course.
Without promising anything yet (we need to sit down and plan this properly) this will hopefully include updated art, some new character models, optimisations, more music, more sound-effects, surround-sound support, gameplay tweaks and fixes, general bug fixes, and story-and-dialogue edits to tighten the pacing a bit. We're also planning to make some cuts...but nothing major, and all of it to improve flow.
You also mentioned getting rid of the books and making it one long, fluid game. Please correct me if I'm wrong, but I assume that this will be implemented in the "complete" version of the game, and when book 5 is released, the book structure of the game will still be intact, and will include an updated version of book 1.