You still haven't mentioned testing or replacing the rotor. This very well could be a rotor issue.
Also, you did some work with the brushes, but did you de-burnish the slip rings with emory cloth or fine sandpaper?
Have you given thought to buying Rick Jones' book? If you had this book your problem would likely be solved by now. Apparently he offers an electronic version now...
Current: 93 R100GS, 03 XR650R
Prior: 73 CB350, 77 R100/7, 83 R100RT, 04 XR650L
I love every motorcycle I've owned and even some that I haven't.