@iceman, This is maddening to me as well. Some things that defy all rules of harmony just sound great when done by the masters. Those guys aren't thinking theory when they play that kind of stuff, just using their ear to come up with something cool. But your particular examples have some pretty straight ahead explanations.
- C on the A7 is just a minor 3rd (or sharp 9) which is straight from the blues scale, a very common thing to do on a dominant 7 chord for a bluesy sound. In fact, that whole bar is mostly the blues scale. Lots of places to add blue notes to a tune like Georgia. The organ solo plays a ton of blues scale licks as well. One thing I like to do is emphasize that minor 3rd in a lot of bluesy licks, then ultimately resolve to the major 3rd that's actually in the chord. Really nice effect.
- G# diminished is a cool thing to play on a D7 (not necessarily D major) as it contains all those juicy extensions (#11, 13, 1 (not so juicy), #9) of D7 and mostly fits Bm (G# is the 6th, which is fine).
(EDIT: After a second listen, that's not G# diminished, it's another blues scale. Nothing crazy going on there either on the D and Bm).
So to really dig into this, learn your blues scales and copy the heck out of his style and how he sculpts his lines.
That's one killer solo by the way. My hat is off to you if you can master that one, especially the altissimo parts. But much more important than the notes are the intensity, they way he builds tension and uses a metric ton of soul. I think this is the recording that matches your transcription: