I know I might be kinda Necromancing this post, but it caught my eye. Sorry!
A lot of Jerry's fingerwork has to do with the interplay between chord and mode structure. The Dead's tunes most commonly used Major and its partners Mixolydian (Scarlet/Fire, Franklins, Dark Star, Birdsong) and Blues (Truckin') and on a rare occasion Lydian (Lady with a fan). They also used Minor and its partner Dorian (Estimated, Other One, Playin').
Jerry's style was similar in some respects to the CAGED method, which effectively teaches you to form a shape (or series of them) over the fretboard (not necessarily fretted) and play scales in them based on where the root is. To do this, you have to get a grasp on what chords work in conjunction with the root chord.
Blues is effectively a minor pentatonic over a major key. There's more to it than this, but this is the basic idea.
I/i have an subdominant option of IV/iv and a dominant chord of V of V7. So in "C major," IV is "F" and V is "G." When not using a pentatonic, Jerry would generally place his second finger on the root, giving you the option of never having to move your hand to play a complete one octave major scale. In "C major" it ends up being (lining each finger up with the 2nd through 5th fret respectively, starting on fist position "C") A string: 2nd, pinkie, D string: 1st, 2nd, pinkie, G string: 1st, 3rd, pinkie. For minor, starting on 3rd fret C- A string: 1st, 3rd, pinkie, D string: 1st, 3rd, pinkie, G string: 1st, 3rd, pinkie. Jerry used this pattern as a sequence, generally.
I/i subdominant with IV and a "dominant" of V/v. In "C Mixolydian" you essentially play the same as you would for major, only you flat the 7th. In terms of fingers, and positions it is- A string: 2nd, pinkie, D string: 1st, 2nd, pinkie, G string: 1st, 2nd, pinkie. And then dorian requires a slight positioning shift- A string: 1st, 3rd, pinkie, D string: 1st, 3rd, (shift so first finger is on the second fret, G string: 1st, 2nd, pinkie. Jerry would also sequence this.
Mixolydian: CAGED hybrid during the solo. Scales and sequences during the Jam. Other pure Jerry licks, too.http://www.youtube.com/watch?v=oFaLw7laS9E
Dorian: Minor Pentatonic and Scales with Chromaticshttp://www.youtube.com/watch?v=skgE2BT2dZc&feature=related
I, subdominant is a II, "dominant" is a V. This scale has a double leading tone. Effectively, we've now raised the 4th scale degree a half step. Again, in C, start like Major. A string: 2nd, pinkie, D string: 1st, 3rd, pinkie, G string: 1st, 3rd, pinkie. More sequencing ensues. Take a look at the "Lady with a Fan" solo. John Kadlecik has some tasty stuff on the modern day outros.
These scales are what Jerry tended to use. He would use a variation of the CAGED method to back and forth between running these scales and their arpeggios in both the "Do, Me, Sol" facet and the "Do, La, Ti, Sol, La, Fa, Sol, Mi, Fa, Re, Mi, Do," way. I like to practice these scales over tunes so they seem to have more application. A lot of both Jerry's and Bobby's riffs in songs are based around these patterns as well. To make the scales even more Jerry like, add chromaticism (generally ascending) in there by blocking the fingers together between the given scale-wise intervals. Final step... listen to tons of Jerry and practice for 10+ hours week!
As a disclaimer... all this means nothing unless you can hear it in your head. Practice playing melodies in various keys and it helps a lot. Jerry might not have sat down and broken down the theory of what he was doing, but there was a method to it that he learned over the years.
When I was younger, this vid helped a bunch:http://www.youtube.com/watch?v=bwhjalRiL8s
JDarks can be a goof, but I learned a lot from them vids. Hope this all helps! Perfectly willing to shoot more ideas out there.