I think it's wonderful that you've come this far already, well done!
When clickertraining or just training a horse to overcome his fears, it's important to always work from the no-problem- to the problem-parts. If you have a horse who is afraid of the trailer and refuses to get in, you start with walking him around the thing - something he isn't scared of, letting him touch it, then asking him to target something and slowly hold the target closer to the ramp until your horse has followed the target into the trailer. In this case you van follow the same approach. As your pony is afraid of getting stuck with her leg around the hoof, you can start teaching her that this isn't a problem by training this on a bodypart that doesn't have problems with this, for example the upper hindleg. It's in fact quite simple: you stroke with both hands from her spine down the hindquarters until you reacht the part where the leg comes out of the body, and in a flowing movement you cup this joint (the knee) with your hands, one hand covering the front of the knee, the other the back. Click and treat. Repeat this untill you're sure the pony is totally relaxed with this, and then follow the same process but go a cm further down the leg while stroking down and cup it there before you click. You repeat this process in millimetres further downwards, in which you always stroken from pelvis down the leg with both hands and then cup the part you want by enclosing it with you hands for a short time before you click. Your hands do not squeeze, they envelop the leg, just as when you place your hands around your upper own leg. When your pony is comfortable with all this, you can rest your hands wrapped around the leg longer on the same place, and finally do this also when the leg is lifted by following the same procedure with one hand while the other one supports the leg.
If you're pony is very traumatized, then this will take some time. Just be patient, supportive and reward the slightest improvement. Also keep in mind that this time you do not click for the reactions of your pony, but for the progress that you yourself make on the leg. When you're patient and your pony trusts you and the clicker, I'm quite sure that you two can work this problem out by using clickertraining.
By the way, problemsolving like this is not something you work on immediately when you start using the clicker on your horse! First you teach her neutral things like targetting so that she gets the point and will decide that she likes this training. When instead you'd start tackling grave problems in the first training session, your horse will shut down and decide that the clicker, although it brings food, means trouble, hard work and fearful exercises. Only when she trusts the little plastic thing, its sound and the fact that this helps her during training, you can start working on reducing fear and even then it is important to keep doing positive exercises too.
