You are totally not alone. I've been playing guitar since high school. I'm 30 now (yikes) and it's only been recently that I started putting everything together to where I have a clue as to what scales go with what chords, etc... The problem is that guitar players have too many choices as to which notes to play and which fingerings to use to play those notes. It stunts your ability to build a frame of reference. That's why you may know your scales, you may know chords, but you don't know how they all go together.