Ultra Sensitive and Over Reactive
I really feel for you and your Yorkie too. Working with rescues and fosters I have some experience with this. I try to desensitze them, by doing what you have been doing, touching in a comforting way. But this doesn't always work.
I am surprized that your Vet did not give her a mild med to calm her down and make her groggy. People are not the only beings that suffer panic attacks. This may still be an option for nail trimming because it only has to be done about every 4 weeks. I would try some of these ideas first.
Nails: 1. try a different tool. If she hates the electric pedi-paws, try a toenail clipper. Or switch to a diamond nail file or emeryboard. You can also wrap a strip of very fine sand paper around your index finger and use it for a nail file.
2. Reduce the time it takes. Do 2 nails and stop and praise and treat. Wait a few hours or a day and do two more. Just be sure you know where you stopped.
3. Use two people, one to hold her and one to trim (again don't prolong a stressful situation. Stop after one foot if you need to.)
4. Some dogs just hate to have their feet restrained and will try to pull away. With these little ones, I have my helper hold them in a standing position to do the front paws. It is good to do this on a counter or on top the washer. Put a bath towel down for them to stand on. You can have your helper hold the dog up and cradle their butt. (nothing is touching the counter)
Top Knot tips. At first just just brush and twist the little ponytail and put a tiny clip on it. 10 seconds done. Do this for a few weeks at least, then go to the band. Be careful not to do the band too tight and don't be picky about getting it perfect at first. It is important to always put the band about 1/4 to 1/2 inch above the scalp. If it is too tight your baby can get a head ache just like we do when our hat is too tight. I hope these hints help.