Get a professional saddle fitter!
I just bought a custom made Schleese and I love it. They make it fit your horse. It can always be adjusted for any horse at anytime
Possibly a thicker or special made saddle pad?
I would recommend Bute, maybe sometimes acupuncture works, and there'll be no problem when swelling and pain goes!
I would be wanting to have the horse checked out by an experienced veterinary to see why my horse is injured :)