well how high is Vai's action? I just took that picture from all about evo.
And yeah, what Jeries said, I can't get this guitar in tune any more. It definitely needs new springs too. I'll search around and see if I can find anyone else
kyle i see in the pic you posted you say the knife edge should be visible from the side,this is not correct,yes you need to see it so you set the trem"flat" but you should then set the trem height according to how high you want the string action,i normally find you can only see the top edge of the knife edge if at all.
what i do is set the trem "flat" with the trem high,lower the trem so i roughly have the correct string height then measure the distance between the tip of the trem arm and the guitar body so i have that measurement for future reference when setting up a particular guitar.
your fretwork is more involved and you could be better letting a pro do the work for you unless you want to spend on tools.