I continually practice playing any new idea or problematic issue until I can sit back down to the guitar day after day and never mess it up. That is my personal marker for knowing it's in my muscle memory. I can watch TV and play it without thinking. Until muscle memory is achieved, assuming “something is missing” elsewhere will continue to puzzle the advancing player.
Muscle Memory is the foundation for everything else I build. If you have to ask me, or anyone, how they memorize the things they play, that says you most likely are rushing into the next stages too fast...and bypassing the most important one - muscle memory.
Everything I teach in my courses, and much more, is from my personal muscle memory. I do not kid when I say I am an “eternal beginner” because everything has to be honed and maintained. It's like a pilot making sure the plane is safe to fly before taking off.
"Muscle Memory" allows me to:
1) Play without thinking about "how" something is played... which develops a responsive approach to the songs.
2) Focus only on personal emotion while playing. How is the lyric best served? Soulful expression, dynamics, bleeding deeply while playing so my notes and chords are expressing anger, or sadness, or being sassy, or excited to play, sneaky, or rambunctious. Whatever the lyric and the band is setting forth will prompt an emotional response.
3) Always listen to the other musicians while playing. They are my harmonic and rhythmic foundation to build on.
4) Listen to the Singer above all issues!
5) Respond to the bandmates' conversation regardless of what I "technically think" I would like to play beforehand. I have to be able to surrender at any given moment.