Shimano Shifters/Brakes

The biggest problem I have heard for woman has actually been that they have trouble reaching the STI shift levers when on the hoods or especially in the drops. The are ways to bring the lever in closer but as you said, it leaves the range of motion shorter which can affect the braking in emergency situations.

But then again, if you are grabbing THAT much brake, you are probably locking up the tires and skidding.

Check out your position and reach to the hoods, if it is too far you will rely on your hands to support your weight and this will put a lot of stress there and can lead to the discomfort you're feeling sometimes. Also, cycling gloves with good padding can help if your position is okay.

Of course the biggest factor will be time in the saddle that will make a difference (hopefully).

When I bought my bike, I test-rode a Trek and a Cannondale.. and that was the main difference that I noticed between the two bikes: the shifters on the Cannondale (Tiagra shifters) felt too big in my hands. As soon as I moved to the Trek with 105's, I noticed a world of difference. They were smaller and the hoods were much softer than the Tiagra's. Not sure how your bike shop is about this kind of stuff, but maybe you can move up a component level on the shifters?

I had a bit of 'web' discomfort on my first ride with the new position (I used to ride a MTB, so switching to a road bike was very different)... but since then, it has been fine.