Sorry to hear about your pain. I've been there, too, and it's no fun. The good news is that there are all kinds of things you can do on a bike to help relieve that pain.

Don't be too hard on your LBS. Bike fit is such a VERY personal thing and no bike shop, even the highest end shop, can tell you 100% what will or will not work for you. For me, it's always a work in progress, adjusting this, adjusting that, as I go. Then, too, your pedaling technique and your posture can also be part of the problem, even on a bike that fits, correctly.

As Aromig mentions, too, it takes your body time to fit into a new bike when you're just starting out. Even after a lifetime of biking, when I switch to a different kind of bike, it still feels a little funny for a bit.

Yes, the best bike shops will know all the more subtle issues with fit and subtle they are, too. For instance, even a tiny difference in my seat tilt adjustment makes a huge difference in comfort and performance. Most of these less obvious adjustments you'll have to work out for yourself, but it's a big plus to work with folks who know what these possible adjustments are, in the first place.

Too wide on the handlebars is a common issue for us gals. On flat bars, I usually have to move the grips, shifters and brake levers inward and then trim off the ends of the handlebars. Not much you can do on drop bars but get a narrower set. As for your handlebars being too high, you'll still need to be the judge of that and the only way to know for sure, is to ride and see. Take their suggestion as a guideline, not as gospel.

Best of luck. Hang in there.