Well.

I reckon I'm about 6'2 or 6'3 and nearly 140 lbs @ 16 years old. I used to lift weights 2 years ago and that was the only time I actually 'exercised' outside of PE in school.

Anyway, next season of school is coming up and just like the previous guy, I also want to join Cross Country.

This summer I do want to get in shape and I'm wondering what parts of my body to work on to help me run faster, and have more endurance. As I previously stated, I'm tall and skinny and my body fat is around 5%.

I'm wondering what kind of foods I should start eating (because normally I eat junk food: soda, chips, cookies, chicken nuggets, hot dogs, buffalo wings, etc.) so I can develop some sort of muscle.

If you're confused about what I'm aiming for, well what I'm aiming for is...
1. I do want to look a little muscular but don't want HUGE muscles... (maybe a 6-pack, more muscles on the arms, broader chest, stronger legs and thats about all.)
2. I want to have good stamina so I could run for a long amount of timing without the need for water or a break.
3. Similar to #1, I wanna change my eating habits from junk food to 'good' food.

Thanks in advance and I'll be looking forward to the replies.

1. You won't gain huge muscles overnight, so don't not lift heavy weights because you think you'll get huge really quickly. You should try and work all your muscles rather than ones that will help you directly, because some muscles might help indirectly.
2. You need to run a lot to build up your stamina. To do it without water you will need to start drinking a lot of water everyday. Especially the day before and the day of a meet, be drinking a ton of water(not just an hour before the meet). YOu'll be hydrated all the time, and therefore won't be thirsty after 10-20 min of running.
3. Start today, not tomorrow. You might not be able to stop eating all junk food, but try to make conscious decisions to eat a healthy snack rather than junk food.

What CrazyCarl said is exactly correct!

One thing, faster (stronger) and longer (endurance) are two totally different things. If you want to get faster, you need to do some sprints... Try Fartlek or intervals at the track. For endurance, you need to run long distances (as CC said).

If you just want to add a little muscle size and definition, try body weight workouts (i.e. push-ups, chin-ups, sit-ups, one-legged squats, one-legged calf raises, handstand push-ups, etc.)

Nutrition is key to this working! Cut out the sodas completely. Drink water instead. Don't eat sugar filled things (e.g. bubble gum, candy bars, etc.)

Start out slowly and progress with time. Today, quit sodas.

-Rip