jerry is hard to pin down, but with jerry im quite sure that his hands weren't really in his mind while he's jammin, he's just listening, and grooving to the music.
the fingers just kinda do what he wants. or what they want, either way we all love it right? i think its the level of expression we all seek as musicians.
when i wanna understand a piece of jerrymusic i like to get in jerrys mind, he began as a folk guitarist, so what that tips me off to is that jerry was big into chord melodies and harmonization. So alot of his runs arent scale wise, they're chordwise (arpeggios) So say you run an apreggio through two octaves 1-3-5-1-3-5 from there if you look at the chord change you you may find you are moving from G to A#, thats a good time to pull a chromatic run to the 3 of the A# and then play that apreggio backwards bending into a couple of the diatonic notes of whatever mode A# happens to be representing.
the idea here is to think less of those chords and these scales, and to understand how he fit it into the piece of music as a whole. Watch how the chords move, look for chord notes that aren't in your scale and you found some of the "jerry chromatics". Likewise like i said many chromatic runs on chord changes.
The second thing is that, jerry's modal sound really comes from the fact that he knows how to use them. He's really bringing alive each chord, and filling the changes to enhance the overall movement.
For example, while moving from Amaj to E7 you may be playing a A majorscale lick over the A , but abruptly in the middle of it before you resolve the phrase, do a chromatic run, or slide or some kind of move into the E7 and resolve it with a mixolydian lick (landing it on E instead of on A, creating a sensation that the musical experience has shifted, not just the rhythm chords or whatever).
a great example of something like this is the verse lick in scarlet begonias, where at the end of the first line its moving from B to A, and he plays that little lick that starts on B and ends on A, where somehow when you play it by itself it sounds unresolved, in the scheme of the music, and chord changes it helps reinforce the musical statement. (except here i think your moving from mixolydian lydian (5 to 4).
okay now im just rambling, but just some ideas for understanding jerry