Many horses get vaccines reactions and I would bet that this is part of what you are seeing. You might want to talk with your vet about doing vaccines in January instead of April and changing the whole schedule.
Horse's bodies make antibodies to fight off irritants and disease. All bodies do. However, some animals make too many antibodies and this presents as allergies. The body's defense system plays a little trick on us and we end up feeling worse. Same works for horses.
There ARE effective antihistamines that you can get from your vet.
Aside from that, I would try to keep her on pasture grass as much as I could. If you give hay, be sure to spray it with water first to minimize the dust that the horse inhales. Also, you should try to get as much ventilation into her stall as you can so that she gets fresh air. You should also get rid of her bedding and use a soft, synthetic floor instead. If you can't afford the panels that the equine stoors sell, try contacting a manufacturing company and see if they will give you or sell to you their old conveyor belts. These work great!
With these horses, you have to be creative and get rid of all the allergens that you can think of - dust, hay, flies, bugs, etc.
I would suggest that you use fly spray EVERY day and tie some downy sheets to her halter around her eyes and ears. This will deter the bugs even more and it makes the horse smell nice.
I hope that this helps more!
Let me know if you still have questions.