whole step

[Pacman]

oh boy I just started a huge mess.... PERHAPS the reason no one gets it is because it doesnt work that way...

I think that's the problem, but I think I know what you're asking.

6 fret on G = C#
9 fret on E = C#

Yes, but they're an octave apart at this point. If you wanted to continue the scale pattern, you'd have to be an octave higher on the E string. The real question is why you'd want to do this. The shift to play the whole scale on the G string would be much easier. Or, you could start out at the G on the A string, and do the whole pattern from there.

 

[MCBTunes]

finally, some clarity .

So what your saying is if the root, is on the D or G string those are the only strings you will use for the scale unless you go way up into the upper register to hit the proper note.

 

[Pacman]

Exactly, if you want to play it 'as a scale'. That is, acending in pitch all the way.

 

[lemur821]

If you want to play across the strings rather than up one then you need to start on a lower string and work up. So if you wanted to play that A scale without shifting positions every few notes you could play:

------------------------------------------------
-------------------------------16--18--19-
-------------16--17--19-------------------
---17-19------------------------------------

or

-------------------------------11--15--16-
-------------11--12--14-------------------
---12-14------------------------------------
------------------------------------------------

That fingering pattern will give you a major scale, and so will other like it. You should be able to find a lot of scale fingering patterns if you do some searches.

EDIT:

So what your saying is if the root, is on the D or G string those are the only strings you will use for the scale unless you go way up into the upper register to hit the proper note.

Oh, you seem to understand. You just have to start at a higher position, or shift there when you get the chance. Or add more high strings, I guess.