The examples are constructed carefully so you ought to make an effort to digest them equally carefully. If you play blindly through each run your knowledge will end up fractured and incoherent. Optimal progress is possible only if you exercise your brain as well as your fingers.
Soloing over chord progressions requires not only that you know which notes fits which chords but also that you know what the next chord is going to sound like. If you are playing over a blues you can probably fake your way through even if you don't understand what you are doing because you have heard the chord sequence hundreds of times. Faking your way through Giant Steps, where the chords descend in major thirds, is a very different matter. Ear training is important so listen carefully to the chords, and in particular make yourself familiar with parallel chords (a major chord paired with the minor three semitones below). Often the single-note run will sound strange on its own so you need the accompaniment to make sense of it.
For each of the three scales, pentatonic, hexatonic, and pentadominant, the examples are divided into seven groups, numbered from zero to six, depending on the movement of the root note (the groups ht1-ht6 and pd1-pd6 are not created yet). Each group contains 24 examples, two in each of the twelve keys. I have recorded all examples with a click track and a piano accompaniment that plays the chords on the first beat of every bar. The piano accompaniment is in the left channel, the guitar is in the right channel, and the click track is in the center. The recordings are encoded in high-quality mp3 format (192kb/s). The tablature is available in four formats: 1) png (a bitmapped image that opens in a separate window), 2) pdf (for the free Adobe Reader), 3) gp5 (produced by the commercial program Guitar Pro 5 that I am using), and xml (MusicXML that can be read by other programs, most notably TablEdit which provides a free viewer. Be aware, though, that the MusicXML format does not include the left-hand finger numbers 1-4).
Patterns. Always look at the visual patterns the notes form on the fretboard. It is much more important to remember the patterns on the fretboard than the fingerings. Start building up a collection of shapes that appeal to you. Most of the examples are based on the regular shapes described in the section on Fretmaps. However, I have exaggerated quite a few of the examples to make you think about why a particular run is mapped out in certain way. Position playing is severely limiting when it is overused (I am living proof of that), and I have deliberately inserted a lot of variation in the way even trivial lines are played.
Rythm. Most examples are played in straight eights, and only a few with the swing (triplet) feel. Some examples are focused on rythm rather than melody. A few exotic runs in odd meters (3/4, 5/4, and 7/8) are included as well. The tempos on the recordings are chosen such that each run sounds good musically. They are not intended as performance benchmarks. You might prefer them faster or slower, and indeed I recommend you try them both faster and slower.
Phrasing. If you play all the notes in the same way, like on a piano, you won't produce a very exciting sound. Slides, hammer-ons, and pull-offs are a great way to inject some life into a simple melody, and furthermore it makes playing it much more fun! The examples contain plenty of the effects an experienced guitarist would use in a real performance. I need to point out again that you must be able to trace and recognize the patterns the notes form on the fretboard when you shift up and down the neck.
I encourage you to make a habit of using the clock notation to visualise the chords and notes. It is a lot easier to memorise 10-5-7-2 than Gb-Db-Eb-Bb.