Interesting that raising your bars, which puts more weight on the saddle, has increased your comfort. Makes me think that maybe your saddle is angled up a touch, making it necessary for you to be upright to get your sit bones to align with the saddle. In my experience, that's a real key. But I take the opposite approach: I have a relatively massive saddle-to-bar drop, and spend much of my riding time in the drops. As a result of a fitting, I just switched to a harder and wider saddle to increase my stability and provide a more rotated pelvis, which straightened my back, opened up my breathing, and gave me a lower position in the drops.