#1
Going up a scale and doing fast runs is a real problem for me picking wise. I don't think its my left hand because right now i cheat and legato it lol. descending i can pick fine and it feels very natural to alternate. but ascending, at around changing from the G string to the B it gets very awkward and i mess up. Im not sure if this is a picking problem or how i move my arm when im going down the strings. Right now im just doing 3 note per string major scale all down the neck up and down and building speed with a metronome, is that what i should be doing to correct this problem or something else.
#2
You should be practicing what you want to play, so if you want to play 3 note-per-string major scales, practice that. As a byproduct of practicing that, you'll develop the technique to be able to ascend, descend, and sequence other scales and patterns, but you will not be quite as good at those as whatever you practiced that was different.

Your practice approach is perfect, however. Playing fast is hard and requires a lot of practive, so it's good you recognize the need to work hard. If I can make one suggestion, though, you said your trouble is changing between the G and B strings. Practice just that change for a while and then go back and try to play the whole thing.

If you can play something legato, a good guitarist should be able to pick it as well, but if you have to use legato to change between the G and B strings, that isn't the end of the world; strive to be able to pick everything, but don't kill yourself over that.
#3
It's really important when you are having trouble with a lick to analyze and say "where exactly in this lick am I having a problem". Well, it sounds like you have done that, so -

1) Spend some time isolating on the problem area, working on just the part where you cross from the G to the B string.
2) Put it to the slowness test. This is something I do quite often when I'm having trouble getting something up to speed. I will set the metronome to something slow, and play in quarter notes with the goal of every note being absolutely perfect with minimal left hand motion, no tension, etc. If its totally perfect in slow-mo, its ok to continue working on speed, otherwise I correct the problems first in slow-mo - the logic being: if I cant get this perfect slow, than how will it be perfect fast!
#4
as for the G to B string problem, it only happens when i start on the Low E string. So im 3 note per string picking a major scale. I don't really move my arm that much till the D string. Then i think i move it significantly when i get to the G to B, and i think thats what throws me off because descending i can pick it and the arm and wrist movement feel completely natural and fluent. Ive been doing the metronome thing, and i practice the right way im pretty sure so i guess ill just keep building speed with the new 3 note per string major scale shapes ive been working on.
BTW Bangoodcharlote i watched the marty friedmen thing on melodic soloing and it just clicked lol. I had been looking at all the pieces with melodic soloing and my teachers been trying to explain to me but this video just showed the awesomeness and urgency of using target notes and arpeggios that now after practicing for a while ill be able to do it very nicely
(and by a while i mean like 6 months to a year to master it ><