@nutty...I wish I were as smart as you when I was 13! And I wish I had somewhere to go to get good advice back then. I read over what you already are doing and I think you've made some really great choices. Good for you!
The average human female at her optimum weight needs 130 gm of carbohydrate, 54 gm of protein and about 23 gm of fat everyday just to maintain body function. That's rock bottom. You're still growing, so don't cheat yourself of the right nutrients. Not getting the proper nutrition right now will affect you for the rest of your life.
What's cool about how old you are now is that your body totally wants to build more muscles. And the muscle fibers you grow now will be with you forever. The other thing that's important to know about your body is making your bones strong now helps you when you're old. And the best way to do that is with activities that involve jumping and running. The exercise was a great decision on your part. You picked good ones! Keep that up! You might want to add planks to your effort. They are way more effective than crunches.
http://exercise.about.com/od/abs/ss/abexercises_10.htm Do a Google search to find different plank positions that address different parts of your core. Your core is more than just your abs, so working on your entire core helps everything, posture, strength and stability.
Right now, you're going to need the protein to feed that muscle growth. Not tons of it, because that's not healthy either. Don't go over 80 gm a day. And when you eat more protein, you need more fruits and veggies to balance out the acid in your system from the protein. You're not big, so you don't need more than five or six servings of veggies and a couple from fruits everyday. Eat a big variety of them all to get all the right nutrients. Eat cooked veggies (broccoli, kale, brussels sprouts) to get nutrients like calcium (for those bones), and raw veggies (spinach, carrots, salad greens, peppers) for even more nutrients. Eat the fruits to get more vit. C, plus they help keep you from craving sugar.
I'm not sure about recommending dairy products. I don't believe in having a lot of dairy. I try to get most of my vitamins and minerals from the fruit and veggies I eat. But I do still like cheese and yogurt. I don't believe in low-fat or fat-free stuff either. The less processed the better!
Another part of you that's still developing is your endocrine system and your brain. And those need fats! Fats are not evil! Well, some are, the kind that come in shortening and transfats. All the fast food places still use the bad fats. Frying in fat just isn't healthy. I know it tastes good, so once in awhile is ok. But get healthy sources of fats in your life. Like tree nuts (almonds, pecans, walnuts), seeds (pumpkin, sunflower, sesame), healthy oils (olive oil, safflower and sunflower) and avocados. Your hair will look great and so will your skin. Butter is tasty, but keep it to a minimum. Don't do margarine!
With regards to your caloric intake, I would concentrate on getting enough of the protein, veggies, fruit and healthy fats. Your current BMR is somewhere around 1650 calories, what you need to take in to maintain your current weight. But you've got growth spurts coming up and you're going to lean out even if you just maintain that intake. All your girly parts haven't fully developed. Allow yourself to grow and fully develop! If you're worried about the extra layers of fat, then how about cutting specific food groups first, like soda, fruit juices, milk, processed foods and fast foods (I don't know if you're eating that stuff now). Those foods aren't helping you at all! And you might choose to cut some total calories one or two days a week, like on days when you're not exercising or aren't so active. But I wouldn't go under 1200 calories at this point in your life.
One more thing...don't let the scale or comparing yourself to other girls tell you how healthy you are. You know how you feel. When you feel strong, you know it. When you feel sick to your stomach, you know it. If your eating and exercise patterns cause you to feel sick or weak, then your body is telling you not to do that any more. Listen to and respect your body!
Good luck with your efforts! Let us know how you're doing!