In the improv realm, I'd recommend getting familiar with the chord scale that corresponds to the mode of the moment. Seems to me that Bobby moves through chord scales a bunch in the modal improvisations. For example, Dark Star is basically A mixolydian, which is derived from the D major scale. The chord scale for D major is D, Em, F#m, G, A, Bm, C#dim. You can also add 7ths, 9ths, sus2's and sus4's etc. to any/all of these. IMO these tend to work best if you keep them in the middle register--you generally don't want to add big fat bass notes to them when you're in the rhythm guitar role.
Another thing I notice when listening to Bobby is how delicately he tends to strike the strings. It often sounds to me like he's hitting the strings with his fingernails as much as he is with the pick. Lots of hammer-ons and pull-offs within his chord shapes too. It all contributes to that liquid sound that he gets.
http://www.highcountryguitar.com recently re-vamped and updated.
Ideal practice tools for improvisation...backing tracks, lessons on modes, CAGED, etc.