As centerfield said, concentrate on building leg strength and your core. For your legs, start hitting the weight room and do lunges, squats, and leg presses. Running uphill and downhill is also good.
For your core, get a swiss ball and a good book of exercises to go along with it. You want to build up all the muscles from your stomach around to your back.
Assuming your pitching coach is doing a good job in getting your whole body into the pitch, your velocity will increase as your leg and core strength increases — and as you “fill out”.
You are at a point in your life where putting on weight probably will be a problem, so don’t worry too much about it. Just keep eating right (lots of high-protein, low-fat foods), running, building your core, and hitting the weights, and eventually everything will come together. By the time you are 18-19 you’ll be throwing BBs!
And yes, long toss is helpful in developing velocity; make sure you are always throwing on a straight / downward plane though (do not arc the ball at long distances). Move back 15 feet at a time, 3-5 throws at each distance, until you reach a point where you can only reach your target on a bounce, then “pull back” by moving forward at the same 15-foot increments. When you are back at 60’, throw 20-30 fastballs; twice a week, throw the last 5-10 fastballs as hard as you can (but under control and without over-strain). Pushing yourself on occasion will help develop your full potential.
I don’t have experience with weighted balls but a sensible program should be of benefit.