I know the answer isn't revolutionary, but just practice the motions you suck at. Neuroplasticity - scientists found that more cognitive cortical mapping was devoted to the hands of musicians in correlation to how much they practiced. Pick up "The Brain Changes Itself" by Norman Doidge. Same principled applied to recovering stroke patients.
In my experience with guitar, if I want to learn a song with complicated fingering and chord progressions, I keep doing it over and over *slowly* until my fingers can do it..then i pick up the pace. I never start quick.
Just do the alternate picking slow, then pick it up when it gets easier - a "duh" answer, I know. : P