If you can stand it, give your new bike a few more days for your body to adjust to the new positions. I know you have some pain, but it might ease up and the longer you wait the more it will become clear where the problems are. New positions can be uncomfortable until your body adapts, and they **may** be really comfortable later!
I'm now holding off on installing the new shorter stem I had ordered after riding my new road bike for a week- I really was convinced the handlebars were WAY too far away at first, all my weight was on my hands, and my hands were going numb. The more I ride, the more comfortable I am though, and my body has gotten stronger and more balanced and now my weight seems to be naturally distributing itself between my hands, seat and feet! No more numb hands. Now my handlebars don't seem so far away at all, the bike doesn't seem impossibly tall anymore, etc. It just took a month of riding for my body to adjust to the new bike and the new positions. I am really comfortable now, I feel like I fit my bike perfectly, and am starting to ride with more power and grace than on the old "comfortable" upright hybrid loaner bike I started with. I NEVER would have thought this was possible, without actually going through it myself. It's weird to experience.