A technique I learned just a few years ago really helped me in playing scales and stuff.
Try doing all your scales opposite to the way you're used to playing them.
In other words, if a scale is normally started with a downstroke..try starting it with an upstroke and continue on that way, going in the opposite direction you'd normally pick. It's really hard when you first start doing it but if you keep at it every time you practice your scales, after awhile you don't notice the difference anymore and you can start scales in any position without worrying which direction you're picking in.