Hi there,
To be honest, that sounded a lot like me in high school. I was injured more than I wasn't. I knew that I had potential based on my jr high times and my capacity to train, but I had difficulty making PRs that I could be really proud of.
Here's your solution*:
1) You need to check his form. Bad form in the #1 cause of injuries in new runners. For efficiency, make sure he doesn't cross the midpoint of his chest with his arms and keeps his upper body relaxed in general. If you don't want him to get injured, stride is key. You don't want him to heel strike or overextend his leg so that his foot is landing in front of his body. Favoring quick turnover over long loping strides is also important. If you aren't sure how he's doing, take a video and analyze it in slow motion.
2) Core. You need him (and really all of your athletes) to be doing 1-2 hours of core per night. Doing the right kind of core is super important though. I did mostly abs and hip strengthening exercises and still managed to get injured. It took me many appointments with the right PT to finally figure out The Golden Routine, but it really works. It involves a lot of planking and work with a resistance band in addition to the general core and hip mobility stuff I was doing before.
If he's getting shin splints, you should have him do 100m x 2 heel walking to strengthen the muscles there. Even if he doesn't have shin splints, this is a great preventative exercise.
3) The pool. You should have him doing all of his long days in the pool to avoid excessive pounding. If you are not familiar with pool running, it's just like running on land, only you are doing it in the deep end of the pool. Soft surfaces are good to, but nothing beats the pool.
Anyway, that's my advice for what it's worth. It might be helpful. I kind of felt obligated to make this post because I really wish that my coach hadn't been so clueless. It would have been nice if I had known some of this stuff without having to learn all of my lessons the hard way.
*I'm just giving some general advice that has worked for me in the past. It might be easier to offer advice if we knew a bit more about him like how long he's been running, what sport he's played before, and what his injuries were. Based on your post, I'm guessing he's most likely a swimmer if he's that fast with little training.