Slow down. Look at the fretboard. Pick a note by name. Find that one note all over the fretboard. After all, that is what you will be doing when you go looking for a note. Pick another note, or go through the cycle of 4ths.
Look at a song chord chart. Go through the song, slowly, playing each note in each chord, in one five fret area. If the chord is a simple major, play 1 3 5 8 (octive), if it has a 7, play 1 3 5 7. Put on the metronome. Slow. Force yourself to keep up with the metronome. Slow the metronome down if you can not keep up, or play each note for 2 or 4 beats. Ok, now go through the same song using 3 5 8 1 or 3 5 7 1 for each chord. Go through a chart playing only the 3rd, or the 5th, or the 7. You will be working on chords and on the notes on the neck. Thus you have a SOURCE for the notes you are looking for, and a PACE to keep up with, giving you a PURPOSE, and I little CHALLANGE.
The reason I say slow, is that, when I usually practice scales, I am playing fast, and not thinking about the notes, it is more of a finger memory exercise. I know the starting point and the mode, but then my fingers take over. To learn the fretboard, each selection of a note on the fretboard has to be a mental exercise, not a finger skill exercise. The instant I am working on a scale or song I know the fingerings for, my finger memory takes over, and I am not thinking notes.
Tim99.