First off, it sounds like you are getting back into it a little late. I personally begin my off season training as soon as the season ends.
For your workouts, be sure to do a lot of long distance running. Start that right now. Also, be sure to do some elastic band work for your shoulder. You can find these exercises on Google, or maybe even on this site.
You will also want to do a lot of core work. Get used to using the medicine ball, arnd really work your abs (ALL of your abs, not just the beach goer ones )
Avoid any time of bench press, whether it be flat or incline, and do not do any military press. These are very bad for the shoulder, and pinch a lot of ligaments in the shoulder. If you feel like you MUST do bench, use dumbells, as they offer a greater range of motion.
When you begin throwing again, start off easy. Maybe 20-30 throws tops. Do not try to throw hard right away. Only throw once or twice a week to begin. Gradually work your way up.