Yah that's exactly what I am doing now and have been doing for the last few weeks... I know HOW to play but not WHY I play certain things.. also I found myself in a tiny little cage of stunted creativity. Since join the site a couple of months ago or so, I have seen my understanding of what I am doing increased with every day's passing.
I agree.. the most important thing to my education was the intervals.. but you know.. I had read about intervals 100's of times before but it never clicked at all until I saw the full, 12-note chromatic scale broken down with each note's "designation".. Then all of that 1-3-5 chord construction stuff and all the other interval related theory suddenly fell into place. I actually had to look elsewhere off this site to find that.. Tonight I had another moment of clarity.. "Modes".
Again, I've talked about, learnt about, played etc Modes almost everyday for the last 16 years or so.. but it never really clicked.. I still just played what sounded right and could hear the bad notes, like you said earlier in your post.. but that actually limited me creatively because every time I heard a particular chord progression using the same order and voicing of the chords in the progression.. I would immediately go to "that" shape and position on the guitar.
I was studying the Major pentatonic scale and listening to how wrong it sounds if I use 1-3-4-5-7 instead of 1-3-4-5-6.. When I play the minor pentatonic it's 1-b3-4-5-b7.. so I naturally figured it would be the same notes except with all the flats raised back to the major positions.. ie. 1-3-4-5-7.. so anyway.. with the notes of the A Major scale (note, not pentatonic) firmly in my mind, as well on the printed fretboard diagram.. hehe.. I decided to try Modes. I slid up from the 5th fret of the bottom-E string to the B note on the 7th fret.. and then I played EXACTLY the same notes as before except starting on the B.. so of course, suddenly I realise I am playing the B Dorian scale... it just popped into my head.. then I made all the connections.
So essentially.. if I said to you "play the A Major scale in the Dorian mode" it would exactly the same as saying "play the B Dorian scale" because B is always going to be the A's number 2, and the Dorian mode is always starts on the number 2 of the root note (number 1)... I think I used to just go.. "Ok.. yeh it's a B Phrygian scale.. and that's supposed to mean something to me??" and then just keep on playing... anyway yeh.. now I fully understand the Modes as well.