Subscribe to the philosophy of training movement patterns and not isolated muscles.  These will work to strengthen the large muscle groups of your legs, hips, back, and shoulder girdle.  Additionally, this will result in an increase of your resting metabolism (more energy) and higher testosterone output.   For muscle building, its good to hit the same muscle groups with multiple exercises.  For conditioning, working opposing parts of the body (shoulder presses and squats done back-to-back with no rest) increases metabolic demand.  What people see in Crossfit is usually the metabolic conditioning circuits that combine weight training, cardio and gymnastics done at high intensity.  The injuries that occur are generally from using weight that is too heavy to be used when fatigued, 

work on getting your squat mechanics down.  Spend some time in your warm-ups just sitting in a deep squat for a minute or two.  Remember to feel your glutes fire first and then drive up through your heels keeping core tight and back upright. 

There are variations. The front squat is excellent but requires more abdominal strength than the back squat… goblet squats are a good first step.  Overhead squats are very advanced as they require active shoulders to be engaged, I would hold off on them but think of working your way up to it 

the back has some overlap with your hips and shoulders, but that’s fine.  Just be conscious of where you are feeling fatigued and program your exercises accordingly so that you are able to do everything with good form.  Focus on pull-ups and/or lat pulldowns and rows to bring your shoulder blades back to a neutral position.   Deadlifts are another great exercise to emphasize that engage the glutes/hamstrings as well, and it appears you don’t have enough iron to hurt yourself with these either. 

First and foremost, keep your shoulders healthy.  The rotator cuff muscles are what keeps the head of your humerus stable in your joint.  Instability of the shoulder when executing other movements may result in a tear of one of these muscles or, more commonly, a torn labrum.  In addition to the stretches and exercises mentioned above, good rotator cuff exercises are highlighted in the vid