Here is a GREAT book.
Introduction to Computing Systems: From bits & gates to C & beyond
Unfortunately, it's not available for Kindle or iBooks, but I read the FIRST edition about 10 years ago. The link above is for the second edition, but apparently there is a third edition due to come out in January 2013.
It used to be the textbook for the introductory computer science class at the University of Michigan, but then the professors who wrote the book both went to other places. It's great because it really explains the LOGIC of computers, starting with how the hardware works, machine language, assembly language, and ultimately up to C. All of those things about bits and bytes, logic gates, etc., made much more sense to me as I was reading that book. Actually, as I'm writing about it here, I'm sort of inspired to re-read it! But I may wait for the next edition. I sent a message to the publisher (on Amazon's site) requesting a Kindle version, but I'm not very optimistic.
Check out McGraw-Hill's website on the book.
Introduction to Computing Systems, 2/e
They actually have some good downloadable material there, including some PowerPoint slides from lectures given based on the book. If you download the first few PowerPoint presentations from NC State, I think you'll get the gist of what the book's about.