I like the suggestion of the Atomic Speed drills that Tony Holler uses. Give them a try. Beware that Holler talks in absolutes, but the reality is that each athlete is different. You might have to make some adjustments.
I suggest that you buy Training the Young Distance Runner 3rd Edition (It's the newest publication date (2014). One important thing I remember is that as young teenage boys grow, sometimes their bones can sometimes grow faster than their muscles so they go through a gangly, awkward stage. That might (or might not) be happening with your son. My training partner's son shot up in height and he couldn't do one curl with a 5 lb dumbbell. He's fine now, but since he didn't work out, he stayed that way for years.
Just an idea... see if he enjoys doing the beep test. To me, it's a fun workout, but I don't know if it would appeal to a 13-year-old. There are apps you can download to run the beep test. Let me see if I can find a link... Okay, here's a video showing how to do it, but there are several on YouTube, including one on how to train to run the beep test.