My best advice is you haven't ridden near enough to change anything on the bike. If you received a proper fit / set-up from the bike shop, then just go ride. When you get 300-500 miles under your belt, then your body will have had time to adjust and at that point you will know of you really want to change parts, or you have adapted to the riding position.
I put 1000 miles on my stock saddle and it hurt like heck the first month, little less the second, and then less the third. Even when I switched, it actually hurt more the first two weeks, then got better.
My hands, wrist, and shoulders all use to hurt...now not so much...my left elbow was sore for two months....now not so much.
Give it some time.