I built my picking technique and synchronization with my fingers. I use Gambale's approach to picking, which is mostly alternate but not exactly. 99% of fast guitarists are using strict alternate picking. You probably have already started with strict alternate so stick with that unless you have a desire for what I think is a slightly better approach. I got a metronome. I did four finger chromatics and triplets with alternate picking.
Basically this means the 1234 - 4321. I did 1234 up and down the neck(that is 6 stirng, then 5 string etc.. than back up, then move forward a fret) moving one fret up at a time until I got to the 12th fret. Then I did it back down. Using the metronome the whole time. I then did the same thing with the 4321 approach. Next I did triplets with the 124 fingers and 134 fingers. I did them forwards up and down the neck and backwards up and down the neck.
Now do all the above using legato! that is only picking the first note and using hammer ons or pull offs as need to get the rest of the notes.
There are many other things I did, but I mainly done the stuff in Vinnie Moore's speed accuracy and articulation video.
Also I propose after much study in the area, that pure speed when trying to play isn't what will make you a clean and articulate player, or even fast for that matter. I propose that muscle memory is much more important to speed than simply trying to play fast but sloppy. Thats why repitition in my approach is always key. If the muscles in your hand memorize every movement, then speed is a no brainer! Many people who can play fairly fast can have a particular run thrown at them that they can't run through so fast. This is because of muscle memory, get those muscles to move almost subliminally and you'll have plenty of relaxed speed.
Next figure out your week spots. Don't know how to sweep pick? Then start learning... and make up routines. I sweeped every chord in the major scale up the neck. So lets take C major.. I started with the Dm arpeggio and sweeped it(forward and then back) then I did the Em, F, G, Am, Bm(should be m7b5 but I played it as m at the time) and then C and still went on up the board with Dm, Em, F, G and then Am to finish. Then I'd do it backwards.. lol. If you suck at bends, do bending excercises.
Now after all this is done, you won't be able to write Steve Vai stuff, but you'll be able to play it in a few months if you keep it up(atleast practice every other day seriously).
Once you gain control of your fingers and pick, you'll notice you can play just a major scale and it'll sound some what cool, cause you can put just the right attack to get the smooth sound or whatever you want.
Its very hard to write everything I did... but you get the idea. If you want to write like Vai, that'll come with time, and you'll need to learn music theory, chords, interval relationships etc etc etc. I don't suggest trying to learn it all at once... work on your speed, technique etc... and once you have that reasonably good, it'll be easy to keep it at that level with moderate practice, then you can have time to study music theory and that whole realm of learning.