The most obvious reason for a saddle not fitting either a horse or a rider is that it is static. It's hard, it doesn't give. When you ride bareback, even with a pad in between, you don't have this problem. Both you and the horse's back are flexible, but when you sit down on a saddle, you're sitting on a well-padded piece of wood. No amount of padding (your half pad won't matter either) is going to change that it is wood/metal/whatever and not flexible. Now I do fully believe that there should be a saddle out there that is comfortable for your horse and for you and barely bothers you, but especially with a horse that is hard to find a good saddle for, it will be even harder to find a saddle good for you both.
What I wonder is why walk and sitting trot go fine for you, but not rising trot and canter. What is it that is getting in your way, the shape and/or depth of the seat, the knee rolls, the hang-up point of the stirrup leathers? Does it make you lose your balance or do you get sore muscles after riding? Another thing to ask is does the saddle really fit on your horse, and is it possible it could be rocking on your horse's back?