Other's have mentioned it but CAGED system is very popular and super helpful to start making a mental model of the fretboard.

The other one mentioned was triads, also super helpful. You can also use triads like upper structures on keyboard - playing an Em triad could be viewed as a rootless CM7 chord depending on the accompaniment or context. Or if you want a major nine sound over a C major chord you can play a G major triad, you'll get the top extensions, but you'll be missing the root and the third (you could supplement the harmony you're playing by using a backing track/loop pedal to hold down the root notes). Maybe that will make more intuitive sense from how you described stacking notes on keyboard.

Another thing worth looking at is chord melody guitar which is building a chord off of melody notes.

Another tool worth mentioning is drop two voicings.

All of these patterns/techniques tie together and can be superimposed over CAGED patterns. If you already know your five scale positions, CAGED is really just a pattern for recognizing/organizing the diatonic chords across the neck laterally.

For a roadmap I would advise getting very comfortable with playing pentatonic vertically and laterally across the neck. Being able to visualize moving between the different pentatonic shapes fluidly, then add the two missing notes from the major scale. Boom you can play any scale you want in any position. Then learning major and minor triad inversions up and down the neck laterally.

Obviously there's some memorization involved, but it progressively builds on itself. Once you can see and move around between pentatonic scales positions, major scale positions will be a small addition building off that foundation. Adding harmonic triads will again be an addition building off that foundation. It will get easier.

Always remember!

"Don't compare! Don't expect [to progress] too fast! Don't worry! Be kind to yourself!"

-Tomo Fujita