This an older thread, so not sure where you are on your quest now. Although I have a masters degree in music, I still appreciate the simplicity of scale and chord diagrams like most guitarists.
This book by Don Latarski is hands-down the best single source I have seen for practical beginning theory and beyond that isn't expressed in standard notation. There are a lot of quick shortcut approaches out there...so, I caution against any system that just puts little black dots in boxes--without chord or scale tones. It's ideal if you start learning why the shapes are arranged the way they are so you teach your brain and fingers how to fish! So, instead of seeing little black dots when you look at guitar in your mind, you want to begin to see R (for root), 3 or b3 (for 3rd), etc. of chords/scales. The Latarski book(s) can accelerate this learning process bigtime.