If you are on a stock Bontrager saddle with no cut out, then I would definitely explore saddles with cut outs next. So is having a saddle wide enough to support your sit bones. For me, the selle italia Diva Gel Flow does the trick. When I as younger I was OK on the terry liberator and butterfly, and brooks finesse. While saddles are expensive to try out, if you work with a good bike shop they may let you test several, or find stores with good return policies. Working with a bike shop may be best, since they can also be sure your position is optimized. Just cuz some young male clerk can't help you, don't rule out the shop. Ask the shop if there is a manager you can talk to, or talk to women in your area to see if there is a pro shop, or shop with a good rep for dealing with womens issues.

REI has a very generous return policy(i.e. you can return used items) and carries several of these saddles (Diva gel Flow, butterfly), so if you don't have a local REI I suggest mail ordering one at a time from them. You need to heal first, and then test one at a time. If one makes you sore, you need to heal before testing the next one. I would start with the Diva Gel Flow, since I have problems with urethral irritation and its the only one I can now use. I have a used brooks finesse I would sell if u PM me, but honestly I don't recommend it since it doesn't have a cut out.

How old are you? If there is any possibility you are estrogen defecient (i.e. peri-menipausal or post-menopausal, or post-hysterectomy) you may an estrogen cream to ride comfortably (this was essential for me). Some commented that you have kidney pain, without UTI or urehtral irritation. Did you say that? Urethral irritation can lead to a UTI and even kidney infection if untreated. You mentioned having padded shots, but being scrupulosuly clean and changing out of your shorts immediately after riding, and washing the shorts after each ride, sometimes with an antibacterial soap, are all important.