Hey guys. It's been a long while since I've asked anything here, but I'll cut to the point...

With my alternate picking, I'm pretty good within using 2 or 3 strings, but when I use 4 or more strings such as in a 2-octave scale, my picking hand starts flailing. My question is what should I practice to keep this from happening? Maybe some 2 n/s pentatonic runs over all six strings?
Try using a mentronome... keep your time, and once you feel you can play at that speed perfectly, go ahead and make the speed go up a bit.

Also, check your form. Make sure your shoulders and arm isn't going into the picking; keep it all in your wrist. Also be sure to check that you don't lift the pick too high off the strings.

Oh, and the metronome helps you stay steady. Oftentimes people speed up as they get farther into the scale, which leads to said flailing.
I would do some 3 note per string patterns that way you are actually doing a different stroke on each string. Two note per string isn't patterns will not be alternative picking unless it's a melodic sequence, but even so you'll end up with a down stroke on one string and up on the next. You can try doing Major scale patterns/runs, arpeggio runs, minor (harmonic, jazz) scale runs, but do it all over the neck. People that just practice their picking higher up on the frets sometimes have problems trying to pick just as fast lower on the neck.