Have you tried tightening the two nuts in picture C against each other, so that they lock on to the thread, then use the inside one to unscrew the threaded rod? If it's in a tapped hole that should get it out.

I wouldn't worry too much about the hand lever. I tend to remove the hand levers on my mill when I'm using it with CNC since they have a tendency to hit stuff (or me) if I don't!