Another beautiful piece. This analysis refers to the bar numbers in the included 6 page transcription which is of the accompaniment only. I have not transcribed the actual solo.
The analysis basically summarises all the scales that Zappa used and at which stage of the piece he used them. The analysis is fairly detailed and not just the scale is mentioned but which particular notes of the scale were used at each stage as this is central to understanding how Zappa constructed his solos.
A central theme of the accompaniment, which provides a significant part of the feel of the piece, is that all the low Ds are played on the open D string. The other notes in each section are played in a respectively convenient position for them, with the D always readily accesible.
Zappa is not just playing modes here, there's some really interesting chromaticism being used. Bars 3 to 10 are basically B dorian but Zappa plays these as a standard blues at this point and only uses B, D, E and F#.
Bars 11 to 16 are G minor where he uses a raised 6th, E and a raised 7th, F#, over the D major chord on F# bass and the unaltered 7th, F over the G minor chord, but the hammering on and off he uses here also sounds the open B natural which throws in a bit of chromatic flavour.
Bars 17 to 20 over the E 7th with flattened 9th he uses an E phrygian so the high G natural contrasts with G# in the accompaniment but he also uses a C# here for chromatic flavour. This E phrygian over an E 7 flat 9 combined with a C# is much clearer when used later in the piece where he uses both the C natural and the C#.
Bars 21 to 28 are back to a B blues where he avoids the Dorian G# and over the descending bass, bars 29 to 32 he plays an ascending B minor, A,B, C#, D even throwing in an A# and finishing with a blues squirm on bars 33 to 36 that uses bends from the fourth, E and using the flattened fifth, F natural so even though the flattened 6th, G natural is in the bass, he doesn't use it in the solo.