If it were me, I'd put a halter and lead on the horse and start with some ground work & desensitizing, completely ignoring the nose/mouth. When she starts thinking and starting to be relaxed I would put my hand up to the place (in the air) where she starts being uncomfortable, and just start waving my hand around, keeping her head towards me (one hand holding on to the halter, and the other desensitizing) back off when she relaxes and rub her on the neck...
Repeat over and over getting closer and closer each time, until you can completely move your hand around her face/moth without getting a reaction. I would quit there if she was really bad, if she wasn't I might hold my hand still for a second by the place she doesn't like then take it away and rub her face, then put it still right on her nose for a split second then take it away (making sure to take it away before she has time to react). If she does react just keep your hand there best as possible until she relaxes or holds still for 10sec. or so.. The more times she can't get away with something the easier it will get.
My 2yr old has been having the same problems, but she's been getting better and better each day. I will say she had one bad episode, but when she didn't win it was kind of a break through for us, everything calmed down after. I've made it a habit that everytime I am with her I'll do a brief session as I know that's her bad spot, I'll rub her briefly, but long enough to know she won't react... Before haltering, after haltering, before feeding her, after feeding her (I have to bring her in to eat so that the other horses won't bully her), before bridling after bridling, etc. etc. Every opportunity I get I take and use it as a teaching spell... Anyway hope this helps.
If at first you don't succeed, try, try again