Im a big fan of Olympic lifts for a number of reasons-I've also found that anything more than a few weeks at a time of cycling on a strictly Olympic training program, I begin to get shoulder and other joint issues. I still use Olympics in my training, but have found that switching to more of a 5x5 basic training template, with supplemental High Intensity work added on, is much easier on my body-the technical nuances of Olympic work absent a good coach to manage your training and to watch the lifts themselves are just a bit much, in my opinion. I'm very fond of Zack Evenesh's programming-its all very fun, strength oriented, but could certainly be applied with a more high intensity/conditining focus. You might try his Bodyweight Strength Training or some of the related stuff. I've really drifted away from any of Crossfit's programming-I'm not sold on the safety or usefulness of no programming or periodization, kipping pull-ups, etc, on the shoulders and joints.
You can find Evenesh's stuff at