First, accept the fact that your genetics are playing a role right now and you will likely develop more mass later in life rather than in your teenage years. Next, develop a plan and stick to it for a long time, knowing your gains may be slower than those of endomorphs and mesomorphs around you. You're an ectomorph if you didn't know that already...welcome to the club.
I encourage you to concentrate on full body workouts, and a lot of them. With that, continue eating like a fiend. You say you eat healthy.
I am not critiquing your routine but you may not be providing your body enough carbs, fats, and proteins to let it build mass (however slowly it may want to). If you worry about losing a 6-pack...stop. Your goal is to obviously bulk up.
Eat as much as you can, workout as often as you can (never working out a muscle group more than once in 4-5 days). Don't do much cardio as you already know. Let me tell you something.
"Junk food" consists of sugar and fat. You need to be eating man food, 6 times a day. 500-750 calorie meals with a 2:1 carb to protein ratio.
Get your fats, get your vitamins, get your nutrients. Also, one of the most important factors to healthy mass gain is sleep. Do you get an honest 8 hours of sleep?
Every night, consistently? Always eat a big breakfast. Always eat a big snack before bed (by snack I mean healthy like a protein shake with casein, milk and penut butter sandwich, etc).
If you've gone 3.5 hours without eating anything your body is breaking itself down for energy. Best of luck to you and try not to get discouraged. Everyone may tell you this but take it from experience.
The routine you get your body used to now will pay dividends in your 20's. You will gain mass. It just may seem slow right now.
EDIT I did write this more for a boy. Take that into account at your liesure. For a girl, I suggest you concentrate on building up the muscle in your legs (girls have natural genetics for great legs).
Do tons of squats, lunges, seated calf raises, standing calf raises, leg press, hip sled, leg curls, deadlifts. Decent weight to make them grow and don't worry about toning them until you think they're actually big.
It's not healthy to try and gain weight. Don't do it on purpose, especially if you're just going to binge on mcdonalds, because your system will get clogged up and you could get severe health problems. If you eat a good amount and a healthy diet you shouldn't be worried about being underweight.
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