Flexibility is the most undervalued of the 10 general physical skills. Very few people look at stretching and mobility work with excitement. It's tedious and time consuming; it won't impress your friends, but what it will do is greatly reduce your risk of injury. The video above is Dr. Kelly Starrett, a physical therapist and the book he references is what all physical therapist learn is normal range of motion. The point that is important is noticing that a physical therapist will tell you that you're okay when your body goes through these ranges of motion. Kelly's taking it a bit farther by saying it isn't enough to be able to do it passively or while lying down but you need to be able to do it in movement patterns, the same movement patterns that we do at Karma.
CrossFit can be physical therapy if you understand these concepts. Address your ROM. Address your flexibility. If you can do this you can heal your body and reduce your aches.