Oh, dear. Please don't use thrush meds like ThrushBuster for a preventative. The only thing I think is suitable as a preventative is a mix of Apple Cider Vinegar and water,50/50. Most preps you find are harsh, kill healthy tissue and make it MORE susceptable to thrush! Also, there is potential that he has thrush that is hard to detect,but is almost never in sound hind feet without also being in the front. A test for that, is if your horses's frogs look like they have a tight crack in the middle at the heel bulbs instead of a nice, wide valley, and he flinches with pressure from a hoof pick probing.
Saddle fit can still be the problem. If it's pinched enough, there could be lingering soreness, no matter what saddle you use until it's healed. Look for dry spots around his withers and shoulders if the rest of his back is sweaty when you unsaddle, that's a good indicator of pinching. Also, palpating that spot, may induce a flinch, further indicating soreness. A good test for the saddle? Take an old coat hanger, take the hook off, and mold the wire to the underside of the saddle, where the suspect dry spot would be in contact on the horse. Then, careful to make sure it doesn't warp in transit, set it on the corresponding place on the horse's back, if it doesn't rest, touching evenly the whole way, then you know the saddle is pinching. And an overly wide saddle may rest on his spine, causing a whole new pain while ridden.
These bruises on his back feet, are they just pink/black spots on his sole? Dark spots are often times just the hoof pigment and mean nothing at all. Pink spots indicate trauma, but by the time you see them, the pain is probably long gone. If they are suspected the farrier can find the painful spot and direct you in the proper treatment for the situation. Again, its usually not the hinds that suffer, but fronts when issues come up.
If it seems his right front is aggrevated when you ride, but not at liberty, there could be some pulled muscle that is aggrevated by extra weight, the saddle, or just a confrmational weakness. The hoof/shoe will shoe unusual wear and a farrier should notice that and investigate. Also, could be an abscess that is brewing and the weight from a rider is once again just enough to make it ouchy. A few day so off probably wouldn't hurt, regardless, to give whatever it is time to heal before riding again. In the meantime, ground work can improve your relationship and keep him fit and willing. Riding a horse that is limping usually leads to some sour attitudes, so it would benefit you to give him a break and look into again if it doesn't go away after a good rest.