When I was learning about film photography, most of the serious learning of the type you're talking about came in the darkroom--varying exposures, dodging and burning, masking, changing development, etc., which led to a greater understanding of what a negative is and does, etc. In the digital world, the darkroom has become photo editing software on the computer, and for most of us that means Adobe Photoshop. Since you already know a great deal about many elements of photography (exposure, depth of field, optics, etc.), the digital darkroom is definitely the place to start your learning.
Unfortunately, before one can begin to understand Photoshop (and the digital darkroom generally) in depth, one must master some basic know-how. One book that gives a thorough treatment of basic Photoshop techniques, but very little in depth knowledge or theory, is the Photoshop CS2 Bible by Deke McClelland. The virtues of the Photoshop Bible are that it is a suitable beginning reference for someone who knows very little about Photoshop, it is easily understandable and it is fairly complete. I don't think it is the type of book you are looking for, but I mention it only if you think you need a basic "how-to" book.
Real World Photoshop by Fraser and Blattner is a more advanced compendium of Photoshop techniques, with a good deal more theory and explanation of why things work the way they do in the digital world. I think it would be a difficult way to learn Photoshop, however, if you didn't already have at least some basic knowledge. Fraser also has a book on Real World Camera Raw discussing the Raw file conversion program that comes with Photoshop.
A book that really makes you think about the principles of digital photography is Adobe Photoshop Master Class by John Paul Caponigro. It contains explanations of various techniques, but I think its greater value lies in the general principles that are illustrated.
Dan Margulis has written two books about Photoshop that are also fairly advanced--Professional Photoshop and Photoshop LAB Color. Both of them led me to some serious reflection about the nature of digital photography.
The book you describe probably hasn't been written yet, or at least I haven't seen it. Depending on what you are looking for, the books above are worthwhile, even if they are not as conprehensive as you might wish, and they will teach you quite a lot about digital photography. As another poster mentioned, a lot of the learning about digital photography is on-line, and a lot of it is found just by asking questions on forums like this one.
Good luck and have fun.