Once again, doing the "boxes" method Pacman talks about here (
Pacman's sure-fire scale practice method) will help with this immensely. Mastering that you can start any scale on any point of the scale on any string and go up and down across the whole fingerboard. You learn, almost as a side effect, all the modes, too.
Breaking out of one box into another seamlessly is another leap I'm just now starting to make, but that is opening up a lot of possibilities, too.