You're putting too much pressure on your perineum. That is, instead of your weight being carried by your sit bones at the back of the saddle, it is being borne by the soft tissue between your legs - you are sitting on the narrow part of the saddle. You need to stop doing this, as well as being painful it will cause you damage.

From your description this has become more of a problem since you adopted more of a flat-backed position. It makes sense that this change has helped your lower back. It will also have made you more aero. But the price you are paying is too high. I'd strongly recommend that you try a new saddle. Those with the cutout centre may help, but it's impossible to know what will suit you, it's largely a matter of trial and error.