Cool. I read your original post again and realized that you already learn stuff by ear.
I'll share with you the approach Dave Weiner taught me.
For one given practice session, pick a key, let's say A. A minor pentatonic.
Spell out the notes in the scale, in this case A C D E G.
As you hammer out the scale in each position, say the note name at the same time, this helps to solidify your knowledge of the entire fretboard. This can get tedious, but it helps.
Next, he stressed the point is to make music! Find a backing track or make one, then practice being comfortable playing in one box, then the next. Then combine, etc.