OK here's my dogmatic answer...
First, understand that theory is all about what generally works- it's not hard and fast rules, but an attempt to explain in a logical fashion what works most of the time. That is to say, there are only two ironclad rules of music theory, and they're related to each other. The first rule is "If it sound good, it's right". The second rule is "If it sound bad, it's wrong". Of course there's a lot of subjectivity in what and who defines "sounds good" and "sounds bad". So understand that theory is simply a way to explain what sounds good to most people most of the time. My grandmother always thought that minor third against a major chord was WRONG, but that's the sound of blues that hooked me on learning music.
Second- Get a copy of "Edly's Music Theory For Practical People" [
http://www.edly.com/mtfpp.html]. I HIGHLY recommend this book because:
A. It's well written with great graphics
B. It doesn't assume that all theory is based on western classical music, or jazz. He talks about a lot of different kinds of music
C. It doesn't assume you play piano or that you can read music ('though he makes a great case for taking the time to learn the language or music)
Many of the diagrams are what I drew by hand decades ago when I was teaching full time (although his are actually legible).
Third- Learn in a logical manner. I think you need to understand the diatonic major scale as the basis for everything else. And "knowing" a scale has just about nothing to do with playing it up and down the neck in 16ths at 180 BPM. "Knowing" in this case means:
A. You know how the scale is constructed- that is, you KNOW it's W W H W W W H
B. You can derive for yourself the names of the notes (correct enharmonics is important) in any key. On paper is where it starts, but it's not hard at all to figure out in your head if you think things through. That means you can figure out that the key of A is A B C# D E F# G#, and you know
WHY it's G# and not Ab.
C. You can find the notes of the scale on the neck and execute it over two octaves at least in a steady tempo in any key.
D. Whenever you play the scale, you know what the next note should sound like BEFORE you play it.
Fourth once you OWN the major scale look at basic chord construction. Learn both from scale degrees (e.g. the major chord is 1, 3, 5; minor is 1, b3, 5; 7th is 1, 3, 5 b7, major 7 is 1, 3, 5, 7, etc.) AND with intervals (major is a major third with a minor third stacked on top, a minor chord is a minor third with a major third on top, etc.) You should learn how to build chords and figure out what notes make a chord in any key for:
Major triad C 1 3 5 C E G
minor triad Cmin 1 b3 5 C Eb G
Dominant 7 C7 1 3 5 b7 C E G Bb
Major 7 CMaj7 1 3 5 7 C E G B
Minor 7 Cmin7 1 b3 5 b7 C Eb G Bb
Diminished tirad Cdim 1 b3 bb5 C Eb Gbb (and why it's a double flat 5, not a sharp 4)
Augmented Caug 1 3 #5 C E G#
Fifth learn the harmonized scale- that is learn WHY the I and IV are major 7, why the ii, iii, and vi are minor 7, why the V is a dominant 7, and why the vii is a minor 7 b5 (and only a diminished if you only go to the triad).
At each step you need to be able to execute this stuff on guitar, but the theory isn't so much about PLAYING this stuff as sit is about knowing how things go together.
This foundational study will allow you to figure out and understand the WHY instead of memorizing the same stuff. LEARN and MEMORIZE ain't the same thing. So build your study so each step builds on the previous one. SING every exercise you play so it's not just a mental and physical thing, but include the all important aural training too.
Have fun too, because it really is cool to be able to see how "Here, There, And Everywhere" is such a tidy composition with it's I, ii, iii progression, to see why Jack Bruce's intro bass line on "Badge is simply the Amin arpeggio, why you can play a three note GBD way up the neck while the other guitarists are bashing out an open E minor chord and it WORKS great.
John