I had similar pain on my first long rides with my road bike four years ago.

I went to the bike shop to discuss this (long story but it was not the shop that sold me the bike) and according to the the length of my body parts and to the charts I should have been fine as it. Still, the really nice owner of the shop decided to flip over my stem, which changed my reach distance by about a centimeter (different angle). No more pain!

I got different handlebars two years ago which give me an even shorter reach and I'm even more comfortable. We have avoided changing the stem. But on my next bike, as it was the case for BleekerSt_Girl, I will definitely have a shorter reach from the get go. This seems to be a regular problem in women's bike fitting.