Flip it (the stem), but keep those bars at the same tilt as it looks you are looking for a very relaxed setup. You may be so upright that you are placing an inordinate amount of weight on those sit bones, but that's just a guess. Perhaps a little drop from saddle to bar will lessen the amount of pressure on that area. If the saddle then gets you in the taint, drop the nose a notch at a time to see if it helps. This worked for me when I eased into road geometry from hybrid and MTB a few years ago.

EDIT: At the risk of messing a Pro fitting, that is. Just saying it worked for me.