When you move, the allergy should subside if he's not getting bitten by the gnats.
I took care of a mare with a very severe gnat allergy and created a very successful regimen that kept her cleared up and happy.
1. When you first start treating, wash the affected areas every day with water and shampoo, and scrub with a soft jelly scrubber. Dry well with vigorous rubbing with a towel (this is where your horse will really appreciate you, lol). After about a week, a lot of the scabs will be gone and will be a lot less irritated (a lot of the irritation comes from the scabs pulling on the hairs).
2. Apply copious amounts of Tea-Pro Wound Spray http://www.smartpakequine.com/productclass.aspx?productClassid=280 enough to soak down to the skin; rub it in if you can. It can be expensive to use so much, but it provides immense relief. And it smells good :)
3. Apply globs of Tri-Care wound ointment on the affected areas. http://www.smartpakequine.com/ProductClass.aspx?productclassid=3496&cm_vc=Search Rub it in very well, your horse will appreciate it!
4. Follow up with globs of Swat. You can even mix up a tub of the Tri-Care and Swat together, you'll be using a lot of it.
5. Douse the rest of the horse in fly spray.
6. Top off with a fly sheet with a belly band that fits close to the skin.
Tips: The ointments will attract dirt. After the first week or so, if there is still ointment on the horse the next day, it's okay to leave it on, because it's providing a barrier from the bugs as well as dirt from the wounds. You can go down to just hosing off or wiping off with a washcloth every other day or as needed. When the scabs are healed, you will just need to slather on Swat, fly spray, and put on the fly sheet.