You're welcome for the reply. It's important to map the fretboard in order to know the location of the musical alphabet & then scale degrees & chord tones. But that will gradually happen over the course of time if you just keep working on it.
And one thing that can help you really concretize those notes & degrees is to learn specific licks; musical phrases to play.
And this is really what you need to start doing to get where you want to go. I have an entire collection of tutorials on building a vocabulary of licks. I can't stress this enough: learn licks. Learn little musical musical phrases that you can use to play as music in real time over a backing track. You can alter them, adjust them, move them up and down in repeating octaves, etc.
https://www.guitartricks.com/collection/Bread-and-Butter-Butter-Blues-Licks
You aksed about the playing the 5 3 1 and 7 5 3 of the respective chords. Yes, he's literally just playing the chord tones. Those numbers are the chord tones. Now all those notes are also all part of the D minor scale. But he's looking at it as both, because all the notes from all those chords are all in the D minor scale.
I think you really need to look at my improvisation course. I explain all of this in depth & detail.
https://www.guitartricks.com/collection/learning-to-improvise
Also, when you harmonize a scale you get a chord on every note of the scale using only notes from that scale. So you can refer to the notes of the chord as the chord tones of that individual chord, or as scale degrees from that scale. So you might be getting confused about the fact that you can look at or refer to it in 2 different ways. But it's all integrated. It's all part of the same system, just referred to in 2 mutually reinforcing ways.
With that in mind you might also enjoy my tutorials on harmonizing the major & minor scales.
Major Scale Hamony
https://www.guitartricks.com/tutorial/2387/next-lesson
Minor Scale Harmony
https://www.guitartricks.com/tutorial/2393/next-lesson
Hope that helps!
