If you look online under Throwers Ten or look up Jaeger Band Exercises that will give you a good start in terms of shoulder exercises. If you have access to a light dumbbell (under 5 lbs) that is what you want to use with the Throwers Ten. It is very important to understand that these exercises are for the little muscles around the rotator cuff....you dont want to do these exercises with big weights. Also it is very, very important to pay attention to detail when doing these, making sure the arm is at the correct angle ect. so that you work the correct muscles.
I agree with what SeanBaseball said regarding running and long toss.
Baseball is a game (whether pitching, hitting or fielding) where there are fast explosive movements for short periods of time. Other than general cardio what purpose does moving slowly for a long period of time (jogging) serv in preparing the body to move quickly? It doesnt really.
There are different ways to do longtoss. I have always liked the Jaeger Longtoss routine. Again, you can find information online. When SeanBaseball talks about "stretching" your arm out he is talking about throwing for distance. Not in the sense of loading up and seeing how far you can throw. But, throwing with an arc on the ball. One day that may be 40 yards one day it might be 50 yards. It will increase with time and as you go. But, no matter how you do your longtoss (if you like your set number of throws, ok) when you are coming back in you want to make sure you are throwing hard. On a line (no arc) to your partner. You also want to make sure you are accurate with your throws. If the guy you are throwing to always has to take several steps either way to get the ball you need to address that. The most important thing (in my humble opinion) is that you throw consistantly. As you grow up even throwing 6 days a week is fine. For now, 3 or 4 days would be great. Doesnt have to be one way of doing longtoss or another, just be consistant and throw.
Another important thing is making sure you are well warmed up before starting to throw, even if it is just a 20 minute longtoss. Arm circles, the throwers ten a quick dynamic warm up, these should all be done before you touch a baseball to throw. My son (who is a freshman in college) does a quick dynamic warmup, sprints, medicine ball routine, arm circles, throwers ten, wrist weights THEN starts to throw. He likes to have a good sweat going before he throws. It doesnt have to be that involved but you dont want to be cold and just start throwing.
If you can have a parent pick up Tuff Cuff by Steven Ellis (the guy who started this site) it is a great guide regarding pitching workouts.
It is fantastic you are interested enough in your pitching that you want to do the extra work most guys your age cant be bothered with. Keep it up. Look up information and do research. Posting video on the mechanics part of this site is great as well. There are very knowledgable people in terms of mechanics that usually reply.