I'm no bike sizing guru, but I have tweaked my bike to make it more comfortable.

A few things to try:
Raise the handlebars a bit.
Move your seat forward on its rails.
Make sure that your weight is on your "sit bones" and not the soft spot between them.

You can find a wealth of information for adjusting your seat and bars here.

The whole site has gobs of info, but I would start with the link.