I understand everything that you are saying, but I am trying to figure out how to actually accomplish this. I guess what I need to figure out is, if I get him to where he is used to the stick and doesn't really jump at it anymore but moves to the touch of it, is that where I really need him to be? And I can see how my "intentions" and energy level will affect how he sees the use of the stick.
Short answer - Yes.
If he's really that jumpy about it, I'd start desensitizing the air around him -- getting him comfortable with you moving the stick in "his space" without touching him. When he falls asleep when you start windmilling the stick around him and over his head, start rubbing him with it, around the back first, then around the neck, hindquarters, and barrel. When he's good with that, tie a string to the end and desensitize the air, again, if you have to, to the string spinning and smacking the ground. Sometimes the noises frighten them, so be prepared for that. When he's quiet there, toss the string over his topline, and later around his legs. CA calls it "flogging with kindness", and goes into extreme detail with the entire process, as well as "troubleshooting".
Ideally, I like a horse to fall asleep when I, with low body energy, can helicopter that string over his body, slap the ground anywhere around him, and completely trace his outline with the end of the stick, including face and flank areas.
You want to keep the pressure on until he stands quietly and shows some sign of relaxation (blinking, lick/chewing, resting a hind leg, etc). Sensitizing will be the opposite - apply pressure until he moves the way you want him to, and then release the pressure as a reward for moving.