Hah well as another 16 year old back row it might be a bit patronising to give advice but I'm a track runner so I can probably help a little at least:
As pointed out above plyometric work is key, however at about this age weights such as squats and deadlift can be pretty helpful to develop the power necessary for good off the mark speed but less effective for general pace unless you're relatively top heavy(?). Acceleration is key to your overall speed but won't actually give you pace over long distance which is your problem from what I can see?
Sprint conditioning is an effective (if painful) way to gain mid-distance speed. Basically just sprint. A lot.
2 sets of increasing sprints (so something like 40, 60, 80, 100m) would probably be more than enough to start.
Hopefully this is kinda helpful.
