Someone showed me a great exercise for this... it works the left hand fingering and alternate picking at the same time:
Start with your index finger on the E string, 2nd fret, and pick downward. Middle finger goes on the 3rd fret of E, and you pick up. Then index finger moves to the 2nd fret on the A string, and you pick down. Middle finger goes on 3rd fret, and you pick up. Continue walking up the strings, alternating between index on 2 and middle on 3 until you get to the e string... then reverse and work back downward toward E, using down/up alternate picking.
Then repeat with the index/middle/ring fingers, and alternate picking (this one will be a bit more challenging, because there are an odd number of picks on each string. Keep to the true down/up/down/up picking, even when moving between strings. Work up to e, then down to E.
Then you can use index/middle/ring/pinky, alternate picking as you go through the same runs.
This is an excellent exercise for developing finger dexterity and strength (particularly getting the pinky to develop its own brain), as well as developing comfort and confidence in alternate picking.
Once you've got a basic comfort with doing this... set your metronome and keep a steady rhythm as you go through these exercises. Speed it up as you gain proficiency.
