I'm a bit of a jazz player, Shakedown, so let me see if I can help you out with some things to work on.
You mentioned learning modes, and wondering how to use them. In jazz, what is actually far more important in soling in using chord tones. What you really need to concentrate on is learning arpeggios, in AT LEAST two different positions and on every string set, for Major 6, Major 7, minor 6&7, and dominant 7, 9, 13 chords. Use your scalar tones ( the modes ) and chromaticism to set up the arpeggios in your lines, or as connections between them.
For instance, in jazz, the biggest chord progression to know ( by far ) is the ii-V7-I move. This is a minor 7 ( the 2 chord ), followed by the dominant 7, and ending on the I Major ( usually a Major 7 ) of a given key. So, say in G Major, it would be Amin7, D7, G Maj7. You would want your lines to emphasize the chord tones of the chords ( A,C,E,G over Amin7, D,F#,A,E over D7, and G,B,D,F# over G Maj7 ). To play over this modally, it would be A Dorian, D Mixolydian, and G Ionian, which are all really just the G Major scale emphasizing different notes.
The other important thing to do is to learn the different jazz forms. Generally, there are four areas of jazz; jazz blues, rythm changes, modal compositions, and standards. Work on blues and rythm changes first; they cover the majority of jazz tunes you will ever encounter. Modal compositions are just that ( think "Kind of Blue" Miles Davis ), tunes built around a specific modal progression, and standards are learning how to really play a song - the melody ( head ), accompaniment, and soloing.
Some absolutely excellent method books to get you started on this would be Jazzin'the Blues in the Blues You can Use series by John Ganapes, the excelent All Blues for Jazz Guitar series by Jim Ferguson, the Beginning and Intermediate Jazz Guitar books by Jody Fisher are fantastic ( www.jodyfisher.com
), and another excellent book on soloing that I have just come across is by Garrison Fewell, Melodic Improvisation for Guitar. This book uses a different concept for building solos, using the arpeggios of the ii minor and I major chord over everything and embellishing upon that. All these books start simply and by the time you are done with them, you will be playing some pretty advanced, very hip stuff.
And yes, like it or not, rock and blues playing, while I love them too, are extremely limited in scope compared to jazz. Obviously, there are exceptions to this rule ( like King Crimson - those guys are OUT there ), but in order to really progress beyond scratching the surface of what is possible, you have to break out of playing rock and blues. I look at music as a form of language, and most rock music is prety much on the order of Dick and Jane books, where as with jazz you're getting into Shakespeare. And just like learning any language, the more fluent you become, the more you increase your vocabulary, the more compelling speaker you can be.