Wow, what a great story!
I'm a new bully owner myself and it is really amazing once they open up and trust you. It's really great that you have taken her from being left alone outside (and almost shot!) to a loving home.
I'll second the benadryl suggestion. My vet also said you could use a zyrtec (instead of multiple benadryls per day). I haven't tried that yet, but it sure seems like you have a good handle on the allergies and other maladies and that they are improving. You may also consider filtered water (depending on the water in your area). It may also take a bit for the grain-free food to really kick in, but if her coat is already better, then that's great.
Welcome and thanks for saving a life!