Hey, there!  Congrats on working through all that material.

Memorizing the fretboard in terms of notes is definitely something that happens over time as you keep using the entire fretboard.  I have a couple of other collections that can help with that.

These tutorials are specifically on visualizing the fretboard.  These are aimed at visualizing & playing patterns of repeating octaves.  So it works more for scale degrees & linear patterns.

Visualizing 1

https://www.guitartricks.com/tutorial/419

Visualizing 2

https://www.guitartricks.com/tutorial/898

Visualizing 3

https://www.guitartricks.com/tutorial/899

Visualizing 4

https://www.guitartricks.com/tutorial/462

Next, these are aimed at learning to visualize chord tones.  This is essentially taking the CAGED patterns & learning to break them down into the fundamental major & minor triads & inversions that cover the fretboard.  The first one is my chord theory tutorial that explains the basic concept.  You might want to just start at the 3rd one that starts in on the triad & inversion patterns.

https://guitartricks.com/collection/triads-and-inversions

Regarding learning the notes versus the scale degrees & chord tones.  You definitely need to know both.  But I find that once I'm actually playing some song or piece of music I've already established the notes as musical alphabet letters.  I actually see & think in terms of scale degrees & chord tones because that's more directly related to the sounds that are happening, or that I want to create while improvsing.

So I might look for the note E, but once I visually identify it, then I'm looking at all the notes surrounding it as scale degrees relative to it for sound options.  That's because the concept "major 3rd", or "minor 7th" is related to a sound more directly than "g-sharp", or "d natural".  Make sense?

Quickly identifying the chord tones 1-3-5 is something that also happens with more practice & use.  That's where my triads collection will help,

I think the missing link here is mostly the time spent in repetitious practice doing it.

You might want to have a look at CAGED for lead guitar.  That shows more on how the chord tones are surrounded by & part of the overall scale patterns.  But even then, all that requires the time spent working on it so it's automated.

https://www.guitartricks.com/tutorial/2619

Hope that helps!