I don't know how much "volume" you've been doing w. the hill sprints, or how you are gauging "intensity" w. the runs, but I've found that a combination of warming up w. walks, skips, tempo runs (60-80% efforts), and the occasional hard run or two is good medicine w. most kids. The skips are deceivingly hard and they promote most of the mechanics you want to see w. the runs without it being "more". I keep notes on times, "volume", and form.
A child does not learn to squat from the top down. In other words, he does not suddenly make a conscious decision one day to squat. Actually, he is squatting one day and make the conscious decision to stand. Squatting precedes standing in the developmental sequence. This is the way a child's brain learns to use the body as the child develops movement patterns. Therefore, a child is probably crawling, rocks back into a squatting position with the back completely relaxed and the hips completely flexed, and stands when he has enough hip strength. This approach makes a lot of sense and can be applied to relearning the deep squat movement if it is lost. -Gray Cook
Lifting Clips: http://www.youtube.com/profile?user=johnnymnemonic2
Warm-ups (all at 20 yards) start with walking high knees and arm swings, then faster high kness, butt-kickers, side shuffles both ways, backwards run with turns both ways, a couple of other different things for variety, and then a couple of timed sprints from the three point stance.
Then we move to agilities which involve different things each day. Some days it's bear crawls, or hopping, or shuttle runs, or hop scotch, or passing routes. I mix this up a lot to keep it fun for him, but mostly just want his body moving in different direction and not loaded with any weight. And we almost always work on his first two steps off the line after these are done as kind of a break before strength stuff.
Next comes strength training. We alternate between upper body and lower body durring the three sessions each week. For upper body we do band-assisted pull-ups and then we do push-ups. Our goal here is 5 BW pull-ups and 20 strict push-ups. We will test these once a month to guage progress. On lower body days we do walking lunges (unweighted) for 20 yard laps. We then do BW squats. Some days we do air squats and other days we use a low box and we always work on form. Our goal with the squats is a perfect 50 reps unweighted. There are times when I throw some different stuff in there to keep him entertained, like broom handle overhead squats, squatting with a medicine ball, or whatever I think will entertain him but still work on what we want to accomplish.
Then comes conditioning. We alternate the hill sprints, sled pulls, and prowler pushes (his favorite). For each of these we start out light; light sled or prowler, or hills at 50% intensity. We shoot for 5 or 6 laps depending on how he's feeling. The last two laps of hills are timed and recorded. The last prowler or sled trip we try for a PR in time or a lb or two heavier than the last time.
Lastly we do some core work. Sometimes we use planks and L-sits, other times we use good 'ol sit-ups. We try to be progressive with these but understand that performance will be different each day depending on what we worked on before it.
That's basically it. Every day has similar goals and exercises, but I switch it up just enough so he stays motivated and has fun.