I have been following this thread with great interest but I haven't commented until now.

The scale syllabus should help:
http://jazzbooks.com/mm5/download/FREE-scale-syllabus.pdf

Here is my view:
1-Learn scales, chords and modes as much or as little as you want
2-Learn what scales and modes go with chords as in the syllabus
3-do not let the above get in the way of your playing

That last statement may sound confusing to some. I suggest you play what you feel from your heart then go back and analyze what you have played, if you want too. In other words don't let theory get in the way of your leads and jams, i.e. nothing is worse than a player running scales as a solo with no melody and/or feel. If everyone had stayed within the boundaries of theory we would still be writing and playing like Bach!

On the other hand the more theory you have the more your musical horizons will expand. That is if you have the ear for it. Remember the same 88 keys were under Bach's fingers and were under Monk, Peterson, or Coreas's fingers.

Learning notes contained in chords is what I would start with first. For instance XeroZero's C# statement, a C# is in the chord A7. A C# in a C chord would be written as a Db and the chord might be C7b9 or a C add b9.

I believe that if you base chords on the major scale of the chord's tonic note then all will become quite clear. If you need help on this just let me know.

I am not an expert on theory but I do know some.

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