Just logged on (after a lengthy break!) and saw your post. I have 2 young fell ponies who are clicker trained, have been since 5 months. They are quite different to work with than my high drive, mature (and deaf!) dog is, and each of them uses the clicker in a slightly different way, but it is great fun to work with them this way, and has really opened up our communication. I rarely don't have treats in my pocket when with them, because they will "ask" me to work through things with the clicker when they need to ie if we are out walking and something scary crops up, they will turn to me, look back, and turn back to me to ask me to let them know if it is ok. Then I can use my clicker (I use a mouth sound) to reinforce them looking at it again, which quickly turns into stepping towards and eventually targetting (if possible) the scary thing, and then it never really is an issue again - in fact with a recent meeting with a "dead" wheelie bin - on it's side on a windy day - once we had thoroughly de-scared the first one they were seeking out the others to target, even when they looked different and had moving lids etc.
The first thing I did with the clicker was STOP my colt from mouthing. Typical boy, he explores the world through his mouth, but was getting out of hand. It took about 3mins for him to learn that "look away" = click = treat. This is the first and most important lesson in equine CT. Sometimes it needs to initially be taught behind a barrier so if they become frustrated before they learn the game, you can simply step out of harms way. Goss now knows without a doub that a) he gets nothing from me if he is touching me or in my space and b) he gets nothing without a click, ever. I can be less strict about random treating with Oya, but it upsets Goss too much if I bend the rules so his "treats" are always after me finding something, anything, to click first. Usually that is simply standing quietly.
Once you have the basic manners, you can work on expecting them to actually step away from you for their reward. This makes it even safer, because you are always bringing the reward to them, they never come to you for it.
Following on from Nettle, I think I would either teach her to target, and hold the target position, so that you can then ask her to target and gradually move your hand where you would like it - but this could be fairly longwinded to work through by the time you have taught the clicker game, taught a target, then taught to maintain the touch to target - or if you want to speed the process up then work with a headcollar and rope. Hold the rope gently, not tight, you want to allow her to move away if she is uncomfortable, but the aim is to reward each step of your hand moving. Stand beside her and move your hand up towards her face. Stop still the second she moves away, hold the position until she is relaxed again, then click, move hand, and reward. Repeat, always stopping the second she shows any discomfort, but don't click until she relaxes again. If you get your hand up further than the last time without her moving, then click before she moves - you shouldn't need to see a reaction beyond the first couple of clicks if you are subtle enough. Move by millimetres, not centimetres
Very very gradually you will find her relaxing as your hand moves towards her, which can then develop into touch, and then move up the face, but start from no touching every single time, because the removal of your hand after the click is probably as strong a reinforcement as the food at the moment.
If you want to turn it round, you could teach her to touch your hand herself, be very very clear on boundaries and DON'T use the same cue as for anything else! I did this with the headcollars, basically teaching mine to run towards me and put their own headcollars on purely through shaping. For Goss it was just a game, for Oya it was more important because she had never been comfortable with being caught, but doing it this way gives her the opportunity to tell me when she is ready to be caught - even now she will usually come straight over but sometimes she just needs time to think. If I move towards her she will turn or even walk away, but if I just wait, headcollar open and give her the "head in" cue then when she feels ready she puts her head straight in quite happily.
Thinking about it, this may be a useful game for you to play too, so that she can clearly tell you when she is ready to be handled and teach her that she does have a choice and you will listen. The process of doing up headcollars also helps her to accept hands around the different parts of her head - or it can do if you want it to!!
