There's a difference between pain and discomfort. Discomfort I expect on long rides. Pain means something is wrong. If you're really feeling pain, then fit might continue to be something that needs more attention. Very small changes can make big differences. For example, a friend had very persistent should pain. He was riding handlebars that were 44 cm center to center. This was what the professional fitter suggested. After all, his shoulders were 44 cm wide and conventional wisdom holds that you match your bars to that. He went to 42 cm on a whim and has had not should pain since.