Stretching is your friend.

I stretch every day for about 30 minutes. It's a mix of just general stretching and some light yoga. It has helped me tremendously. Remember, everything is connected. Having your cleat in the wrong place can put too much strain on your calves, which them pull on your hamstrings, that pull on your lower back.

This video is long, but it's got a lot of great information about flexibility, fitness, pain and bike fit (and it comes from a legitimate medical center): Bike Fit: It's All About the Bike - YouTube