Salmon's not a bad protein choice, as far as allergies go. You can also try duck, bison or venison (I'd keep him grain free). Taste of the Wild is a good option.
3X a day seems high, for Apoquel - it's usually one or two, I think. It's also a temporary med, and you should see results quickly. The fact that you're not, leads me to believe the allergen is still present. Food is the most likely culprit, so I'd start there. Remember that treats count too, so make sure they're grain-free and duck or one of the alternate proteins as well.
Watch the scratching, and put him in the cone of shame, if necessary.