I got a new Brompton last week and fitted it with a new Brooks B-17 saddle, and am feeling a bit of pain. The saddle is new, and hard, and needs breaking in. My other bike also sports a B-17 which has a few thousand kilometers on it, and is very comfortable.
The main cure for saddle pain is 1 part adjustment, and 3 parts time. You need to make sure your body is broken in before making many saddle adjustments, even a perfectly adjusted saddle will cause pain if you haven't been doing much riding.
The area I think the OP was describing was his perch a.k.a. 'sitz' bones; the bony protrusions on either side of the 'taint.' Those being the spots that support your weight when you sit on a saddle. The sensitivity of that area, and the need to acclimate it slowly, is the reason why you can't just hop on your bike and start doing century rides. Start with short 1/2 hour rides and slowly work up as your 'butt' gets used to it.
I can't see where the OP ever mentioned using cycling shorts.