[Question] What are some efficient ways of internalizing scales across the neck.

After waiting far to long (like, years) I’ve finally gotten tired of hunting for notes. I’ve started the journey of truly nailing down all of my scales and interval if relationships, but they’re is a lot to cover.

From using an app that displays random notes along with a metronome, can grab any note on any string with a high degree of confidence and I’ve become fairly comfortable with the exact shapes of the major scale intervals. For example I can grab an A on the D string and easily see the major thirds within an octave up or down. I can easily play the major scale in the standard shape, with the roots on the E strings, but I sometimes get lost when am trying to shift positions or weave between scale blocks. I think I benefit a great deal from highly structured drills. What are some methods to best internalize the WHOLE structure of a given scale across the neck without leaving out any permutations? As it is I can grab a note in a given scale but I’m kind of hoping it’s the one I want rather than knowing it’s the one I want.

I think I learned guitar backwards, rushing ahead to licks and phrases, but then having to painfully work out where each note was when I really should have nailed down the fundamentals first.