Does your bike fit? Does your bike hurt you? Bad bike!
Riding a bike should not hurt or cause pain. Your bike should be your best friend and you and it should be having a good time together.
Unfortunately this is not always the case. The biodynamics of cycling can cause pains in quite a wide assortment of body parts.
Just as your bike needs all the parts correctly installed to function properly, so does your bike "fit."
For a couple of decades the science (technology? mystique?) of bike fit has been developing. Many of the top end bike shops have trained technicians who can assess and improve your position on the bike.
The New York Times newspaper took up this subject this week. Read the article here.
Locally, we know that the Cycles Gervais Rioux shop does bike fit, and we are sure that other shops do also, especially if they sell high end bikes. No matter what shop, when you buy a bike there should be a step in the purchasing/delivery process that includes bike fitting adjustments for your unique shape and size.
You might want to ask them what "system" they use, it should not be guess work!
Read more on this subject here, with the google.
If you want to experiment on your own, you should start by writing down the details of the present setup, so you can make adjustments, and keep track of the changes. Park Tools has a bike fit checklist here. Thanks Park Tools!
Good luck, have fun, and if nothing else works, there's always recumbent bikes.