I came here with a question on these exercises, and I see that there are lots of questions. I can clear up a few things first.
I've been starting these exercises on C, 6th string 8th fret. Then all the notes in the major scale have no sharps or flats. C get the number 1, D is 2, E is 3, F is 4, G is 5, A is 6, B is 7, C is 1 and we're into the 2nd octave with the different scale fingering pattern. When we arrive at C on the 1st string 8th fret, we play the D as Justin suggests and then start down.
On the way down the numbering goes C is 1, B is 7, A is 6, G is 5, F is 4, E is 3, D is 2, C is 1, B is 7 and we carry on down to C then B then C.
When we do a different pattern, the numbers stay with those notes. So 1321 is C E D C, and so on. As we go up a scale we count up, as we come down a scale we count down.
When we have one pattern in one key mastered we have a choice to go to a different key with the same pattern, or do a different pattern in the same key.
I found it interesting that by mastering the major scale pattern in C, I would make mistakes when I started on A or G. So I practiced that.
And then I mastered a second pattern in all keys and I'm getting close to a third pattern and a fourth pattern. So I'm getting close to bumping the metronome up.
The question I have was asked by someone else above. I found it easy to do alternating picking on the major scale. And I can start the major scale with either a down stroke or an up stroke and I can do alternating picking either way. Some of the other patterns are not so easy to do both ways. I find myself getting tangled up in my alternating picking when switching strings. Sometimes two up strokes or two down strokes is quicker and easier. So the question is if alternating picking is to be strictly practiced at this point?
But my goal with these scales is to learn to pick the right string at the right time, and use minimal motions with my fret hand. But no more than 5, maybe 10, minutes of scales per day - or else I would go crazy.