Hi OP, I have a rising 3 yo, and had very similar issues to you. The first time the farrier came, a couple weeks after I brought her, he asked me you show him how I pick her feet up and I (embarrassingly) wasn’t able to because well… I was scared of picking them up, she was young and almost completely untouched before I brought her.
When he first sore her he called her ‘wild’ and after much stress he only managed to file her front 2, because she was so stressed. And booked to come back in 4 weeks, to do the back two. He told me what I needed to do, and I worked so hard with her every single day, consistently.
When he came back 4 weeks later, he was in complete shock, she was a different horse, he was even able to do all 4, she stood there beautifully, and unlike the previous visit, that took an hour, and lots of stress, this time it took him 20 minutes, no stress.
So he told me to do these things:
-Firstly I would STOP picking up her feet, and picking them out altogether, and go right back to basics, as the moment it’s just a vicious cycle of - stress for her - stress for you - stress for her - stress for you and it will not get better, she will just resist it more and more, and will feed on your stress also.
-Put a rope tie up in her stable and bring her in and tie her up in the stable twice a day (or every single time your at the yard), so she gets used to standing there and relaxes (this could take a week or two) do not move on to the next step until she’s calm standing there, making it a positive experience
-once she gets used to this routine I would start rubbing my hands down all 4 legs, keeping it very short (around 2 minutes in total) and stopping while she’s still in ‘relax’ mode. I would keep doing this until she is completely comfortable and relaxed every time
-then I would continue rubbing down and 4 legs, and pick just one foot up, and put it straight down again (don’t pick) before she gets a chance to stress. Once comfortable with this, I would do it too two feet, then 3, then all 4
-then when she’s totally comfortable with all of this I would gradually add in picking them out, again one at a time until she’s totally relaxed either you doing it