The key things here are as much mental as physical training.
1. Get him to accept that he will never have a "beach" body. There is nothing - and I do mean nothing - more damaging for a fast bowler than having large amounts of pointless muscular bulk on their upper bodies; all that weight does is pace additional strain on the lower limbs and cause stress fractures and knee problems. Don't believe me? Look at Chris Tremlett, Simon Jones, Shane Watson etc.
2. The biggest key is a repeatable action. This is gained by bowling a lot, but not by over bowling. The latest ECBCA guidance is that under 19s should not bowl more than four days in seven, and at most 14 overs per day - he'd be well off when netting, doing so in a way that recreates a match situation, so bowling six ball sets with three to four minutes inbetween.
3. Cardio. He doesn't need to run enormous distances, but a couple of moerately paced 5ks a week would be beneficial.
You asked specifically about getting more pep in his short ball. He can work on the right muscles using a medicine ball, trying to propel it into the ground acrosds his left hand side, which will give him a little more strength. But in many ways it is as much about getting him to think about where he wants to stick it - he needs to have three varieties of short ball ideally - one that rears from just back of a length to around the nipple area, one that goes through slightly higher and a genuinely quick bouncer (often best delivered after the high one).
And if he is really that good, get him to a club where he will get the necessary support and coaching pathways...