Steve, thanks for the comments and suggestions!
You’re right, and I think I phrased it wrong above: it is not so much trying to learn all the notes, as it is “given a note at random, being able to quickly find one or two positions for that note”; some come more easily, like if I’ve been practicing a scale I tend to at least know where the roots are. That said, I really like your suggestion of focusing on the notes on the 5th and 6th strings, as these are key to power chords.
Actually, no, unfortunately for the two power chord songs I studied well and recorded (Iron Man and Pretty Fly), I learnt the fret positions by muscle memory, but without consideration to what chord was being played. So yeah, I have some things to correct here 
Additionally, I’d like to say that I’ve been through your learning log (or parts of it, because it’s HUGE) and found it very interesting! I like how you structure your learning, they way you allocate time every month for classical guitar - I could probably use that same method to have some set time for some parallel courses, like “practical music theory” for example. Oh, and I really dig your AVOYPs, and how you manage to play and sing at the same time (that’s a skill I have not yet developed); specially enjoyed Morning Has Broken (long time Cat Stevens fan here)