You are taking the right steps. It sounds like you have been very diligent in training your puppy and caring for her especially with a broken foot and quarantine.
If you specifically asked the Vet how she did and he didn't say anything until now that's really disappointing - I would look for a new Vet but at the very least I would stay with her through the visits.
I agree with Ember's comment.
Good luck with the fear trainer.