Hang in there, it's a step in the right direction for getting her used to being handled better. One thing I do know is it's better to work with a bird away from his/her cage. You've got her stick trained which is good, now take her somewhere where she can't see her cage and practice commands. I would use the back of a chair and practice "up" & "down" first with the stick, next with your hand. Once you guys have that down blocking her cage from her view back into her cage and do the "up" "down".

My amazon is handicapped and is afraid of hands. John has gotten her to the point where sitting on the couch he can scratch her head. We've got a huge shelf in her cage that's padded for softness that she uses 90% of the time now, plus we uses thicker perches in her cage as well (hand rails are thicker & flatter). I'll see if I can get a good pic of her leg for you guys.