I'd have to agree with the 5/3/1. You may be able to get stronger faster from other programs, maybe, but 5/3/1 is really laid out to let you maintain/build conditioning level while building/maintaining strength/hypertrophy/etc. Would probably be a good fit if you're looking to build strength without lossing all of your conditioning (which is pretty easy to get back, but since you're a crossfitter and conditioning is your lifeblood so far, it may be a difficult barrier to hurdle).
Another thing to look at for the shoulder is try higher bar placement on the squats and/or moving your hands wider during the squats. This can help relieve some of the problems. It could also be somewhat of an overuse type problem if you're doing cf and following the mainpage or some similar blanket mass programming.