I started a thread here trying to say there's a momumental difference between "teaching"--"do what I tell you and just shut up and ot will make sense later"--versus leading one to discover. I asked that perhaps a methodology could start with a song and have us play a scale in context. That might take a while to develop that but it could be very effective. I think I got the "nice idea I'll pass it along" treatment one gets familiar with whentrying to crusade for change where motivation must always be the horse before the cart of learning instead of the authoritarian model of place the cart of learning before the hores or motivation. What's working for me now--even though I'm glacial at finding the notes in the game where they plot notes on the fret board was to pick something advanced that I really like and solve problems slowly.
I chose "Change the World" by Clapton which I picked up from YouTube lessons. But the version on GT by Doug Showalter is the real deal. At first I encountered a chord that he called out which seeemed tabbed wrong and I got that feeling that here we go again--an error early on that makes you lose trust in the whole thing. But the music that is written was not done by the teacher. I checked all his lessons and he calls out the notes and plays them. When I encounter something that through me a curve I look at the chord name and then go to jguitar.com where you can put that chord in and see all the versions of it and listen to them both strummed and arpeggiated. They are also plotted on the neck. The internet probably has an answer now for everything. I don't think I can just play scales out of context for an hour just for discippline. But if I can find a song or etude that tells me that it involves whole or part of a scale, I will play it, I will find where to play it in another octave and so forth. I so identify with your story and I don't see anyone running to the rescue with the answer that appeals to my sensibilities. But with all these aids and some discipline, you and I can probably DISCOVER through our own detective work and deduction how and why things are the way they are. No one has told me how to know the fretboard. I may have to find a neck with all the notes plotted that someone up loaded and use it to keep up with a teach like Doug who will do a lead and call the notes where unless its down in the open chord area where I spent most of my Kink and Who guitar life, I have to pause and rewind and hunt and peck like a typist who never learned to type. Maybe some of us just can learn unless everything answers a "why" in the immediate sense. Maybe not. But that's me. Good luck.