I've been playing for about 20 years & studied for about three of those. Most people seem to like my playing & I can usually jam with the best of them. Here is my problem though:

When I was studying years ago, the way I was taught got me stuck into knowing scales, modes, etc. in "boxes" and I have a hell of a time seeing the entire fretboard when I'm improvising. I need to learn a way that opens up the fretboard in more than just positions & boxes.

Is there a good book out there can that help me break this habit?

Have you checked out bassbooks.com?

I just bought a bunch of books--fretboard alchemy, bass encylomedia, etc--they have some great stuff; you might be able to narrow your search there.

I took a spare fretboard and labeled the chords in the right positions with black letters. Capitol letters for the main chords and lower case for flats/sharps. I just fret the thing and keep it hanging by me for quick reference. Interactive Bass is a good program for the computer, You play and the notes through your sound board and they are highlighted on the fretboard.

Not a book, but very effective:

http://www.absolutefretboard.com/

Work on sight reading you have to know your fretboard so your not taking your eyes off the music all the time. Also start working on playing two (or more) octave scales and arpeggios and need to really know the fingerboard to do.

You don't need a book, just your brain (and maybe a fingering chart). If you know where the notes are on the neck you can learn scales, arpeggios, and anything else you want and figure out every possible way to play them on the fly.

My problem with guitar and bass education is that people put a lot of emphasis on these "shapes" and "boxes". Not saying they're worthless but they can be very limiting if you don't know how they work. More often than not they're showing you one (not necessarily bad) fingering from root to root - a good place to start but not that helpful in the long run. Again you need to use your brain. If you're running any sort of exercises you need to do them in as many ways as possible. Like Pacman says, don't play until you run out of scale, play until you run out of bass.

Optek Fretlight guitars have an L.E.D. fretboard that will do what you need.

I found Pacman's sticky up top really helpful with this.

http://www.talkbass.com/forum/showthread.php?t=50170

Which I guess follows from EADG mx's post

Try working on scales, not just vertically but horizontally. It's essential to know all of your positional patterns that are played vertically (across the strings) but you want to be able to connect them horizontally so you can move up and down the fingerboard. A great way to get this together is to practice your scales on 1 or 2 strings only and play horizontally (up and down the neck and vice-versa).

One of the benefits of the bass (in standard tuning) is the symmetry of the fingerboard. Once you start breaking things down in to small chunks of information (e.g. 3 consecutive notes from a scale) you start to see that information you already have committed to memory is duplicated all over the fingerboard.

try practicing scales and arpeggios with the notes in order but with big leaps tossed in at random across and up and down while saying the notes out loud and not looking at the neck too often.2 minutes per scale per day should do it