The thing that really helped me with this obstacle was learning how to connect scales across the fretboard using the CAGED system. You learn five major scale patterns based around common chord shapes, and you work to connect them together.

Ben Lindholm and Andy Gurley both have great tutorials on this topic. It really does make a difference in helping you connect your scales, and from there you can better improve your runs and knowledge of the fretboard.

Ben Lindhom - CAGED Tutorial

Andy Gurley - CAGED Tutorial