I'm beginning to believe that once you're in the ballpark, fit-wise, that just riding a lot helps your body adapt to the bike position. As long as you're not straining (mashing, or grinding along at low RPMs in high gear), you'll get used to it. Riding 400-500 miles with a new change in fit seems to be required to really test it out. Most discomfort seems to go away in that time, for me at least.

Of course, YMMV, and if your pain gets worse see a better fit specialist and/or a sports medicine doctor, etc...