I'm 5'3" and whenever I talk to an LBS person about bike size, without mentioning what I currently ride, I'm immediately told that I need 49cm or less. I've also read and been told that top tube length is one of the main measurements you should be concerned with. The fact that you're uncomfortable in the shoulders and private areas might mean you're too stretched out by riding on a too-long top tube. When you say "private areas", do you mean the pubic area up front, or areas farther back? If the discomfort is forward, that sounds as if your weight might be too far forward, causing you to lean heavily on your handlebars and the front of your saddle.

All of the suggestions you've gotten here are possibilities, but it's hard to diagnose this stuff over the 'net. Can you either go back to the guy who fit you, or find someone to give you a second opinion on the fit? A good bike fitter should be able to help you figure out exactly what the issue is, as well as help you tweak your position on the bike.