Understand the major chords in 1st position. Then barre chords based on E and A strings. Then the common inversions of chords (the "D shape" up the neck). Understand what is happening between the notes in that basic "D shape" (intervals).
Pentatonic minor scales. Learn in 1st position, say in the key of A. backwards, forwards, in your sleep. Then 2nd, 3rd position, and so on. Then learn for all the notes. Learn where the root, 3rd, 5th of each position are. Then b3, b3 and so on.
Jump from 1st position to maybe the 4th one...jam. Over and over and over. Slowly build complexity and patterns (triplets etc...small runs, then longer ones, between positions). Move to other kinds of scales, doing the same. (suggest pentatonics because it will be more rapidly useful in general rock music, perhaps keeping someone more engaged. Major scales did crap for me til I was able to integrate them with other scales used more in popular music).
In time, the SOUND or FEEL of the interval will tell you what it is and you stop thinking "oh, where is the 3rd off this, I'm in the key of B...". You have to stop and think what you're doing to WRITE it or explain it to another, but the principles of what you're doing are sound.
Not too many guitarists bop around the 10th fret all 'note conscious'. SOME do, but many more know the basic relationships between root, 3, 5 based on patterns. Unless you're trying to be Steve Vai, I'd try to find some place that feels good and makes you happy. And allows you to communicate your ideas effectively
My 2 cents.