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The way I learned, which I’m not saying is the best necessarily but it got me to a certain level) was completely not shape-oriented, it was sound-oriented, based on the music I was trying to play. So wherever I was on the fretboard, if I wanted to go up a minor 3rd or a perfect 5th, I’d 1) hear it in my head, 2) try and find it, and 3) remember that intervallic shape on tFB. It’s a bit haphazard approach and probably a slower method technique-wise, but I think maybe it helps me to play what’s in my head without playing well-worn shapes.
Try playing the the scale on one string.
... instead using your third or fourth (or maybe your second or third) fingers, just slide your first or second finger up and, voila!, you’re in the second pentatonic box.
To add to your confusion...here's my tuppence worthI had a bit of a breakthrough recently in this area recently. Basically it revolved around noticing when I was back on a root note when running a scale and noticing that from that point the pattern can just be repeated. As long as you know where the roots are the others are easier to work out. I found thinking of the scale formulas in tones/semitones worked well with this. A whole step is 2 frets, a half is 1 fret.The minor pentatonic in tones is 1.5 (3 frets) - 1 (2 frets) - 1 (2 frets) - 1.5 (3 frets) - 1 (2 frets) Totalling 12 frets or all of the diatonic scale bringing you back to your root note if played on one stringSo whenever I hit a root note in a position I know that 3 frets up on the same string is the next note in the pentatonic minor. Once I could see this, I could see more easily how the different positions fit together.When going between strings, there's 5 frets difference in tuning between the EADG then 4 to the B and 5 again to high E. Now I may be a bit weird but I just do a quick bit of arithmetic here.If I'm doing an A minor pentatonic on the 6th string it's the 5th fret, now the next note is C, 1.5 steps, 3 frets away on the 8th fret. If I change string to the next one down then I can take away 5 from 8 and get 3, the 3rd Fret on the 5th string, which is C...