I couldn't read through this post too thoroughly, as I think some of it was a battle of opinions, but I saw a few good points being made. My two cents, is Always End On A Good Note.
Furthermore, Set goals, every time your goal is reached, end your training session
Some of your training sessions will be as simple as clipping a lead rope on her halter. This could take as long as hours, or as short as 5 minutes. Once your goal is attained, gently, GENTLY praise her. A soft hand on her neck, and a soft voice reassuring her as you unclip the lead. Slowly back out of the stall, careful not to startle her, then close the door. She will begin to learn "Hey, this ain't so bad!" and you can start expanding your goals, this time incorporating clipping the halter and leading her around her stall.
Always leave her wanting more. If she learns that turning her butt to you will get you to leave her alone, she will -ALWAYS- do it. Let her know your boss! =)
I trained a completely feral 9 year old Walking Horse mare this way. Her owner couldnt believe it. I had her from feral, to willingly and unaided being loaded into a horse trailer.
Stay patient, and don't show fear! Be bold hun!
Good luck! Keep us posted!