Personally, I'd recommend Basic Elements of Music Theory for the Guitar
by Aaron Shearer if you need the very basics of scale and chord construction ($10 at Amazon), and then McFadden's dissertation/book mentioned in one of the posts above. That's free if you download it from (chapter three is the book): https://tspace.library.utoronto.ca/bits ... thesis.pdf
The more I look at McFadden's work, the more I like it. The first part is heavily oriented toward getting you to learn the fretboard and making sure you understand the basics of theory. If you will actually do all of the exercises, you will have the fretboard down stone cold. The following theory part is extensive and guitar-specific; the latter mostly means that you can play all of the examples and that the exercises are designed for the guitar. I suspect that there's really more theory than most guitarists would ever care about.
If you finish McFadden's book and want still more theory, get yourself a keyboard and Allen Forte's Tonal Harmony in Concept and Practice
. Forte is a major music theorist and the book was written as an undergraduate text. It is by far the most intelligible explanation of harmony theory I've ever seen (for art music - jazz/rock/pop/folk/etc ignores many of the classical rules). It's actually readable even if you don't have a piano, especially in conjunction with something that covers the same material in a guitar-friendly fashion. It's out of print, but is reasonably available from used booksellers on the net; get the third edition, if possible.