Are you looking for strength (i.e. planning to compete) or more for muscle and leanness? Your leg day would be great for a bodybuilder, but not as much for a power lifter.
In either case, recovery is the key for building both muscle and strength. A simple principle would be to alternate intensities and volumes per major lift (easy-hard system):
Squat Day One - heavier weight, but lower sets and reps, strength day, lighter weight assistance stuff, and don't get too carried away with it.
Squat Day Two - relatively lower weight, but more reps, hypertrophy day, so blast your legs with the assistance work if you want
Deadlift Day - you can insert this any point in the week that works for you, but aside from maybe some leg curls, don't bother with any assistance work. Get your strength work, some speed reps or deficits and get out.
Upper body can follow a similar split. I don't know what your particular shoulder issue is, but typically, too much heavy benching will aggravate it. One heavy day, is plenty if you aren't looking to compete. I you are, your second day should be lighter and technique-based. Lots of dumbbell work (rows especially) and tons o' triceps will put on the muscle you need to improve while keeping shoulders in a little better shape.