Don't go for long-distance runs. Please.
What that will do is train your body to endure instead of produce explosive power, which is what is needed for a strong vertical jump. That kind of endurance is basically stringing out your energy over a long event, while jumping takes place in under a second. They're at different ends of the training spectrum. Thus, long distance runs have no carryover to jumping, unless you drop a lot of fat (you'd probably drop a lot of corresponding muscle if you lose your fat through long distance runs). Either you train astounding power or endurance, and if you really want that 40 inch vert in a couple of years, you need to focus on that.
Power comes from having a lot of strength and applying that strength at a fast rate.
Explosive stuff would be plyometrics (applying the strength at a fast rate) and heavy weights (strength training) lifted with a concentration on moving them as fast as possible.
For plyometrics, stuff like a couple of sets of 30 or 40 yard sprints would be beneficial. Ideally you'd want to do these sprints until your speed noticeably drops off. Allow for around 3 minutes rest each sprint, and you shouldn't be huffing and puffing when you begin a set. You can interchange sprints with jumping exercises such as stiff-legged calf jumps, stationary jumps from a squat position, and jumps for max height. Tuck jumps and double leg bounding are also good options.
Don't combine this all on one day. Ideally you'd want it M/W/F, but even M/F is a'ight if you can't swing it.
Monday:
Dynamic warmup
30 yard sprints x until speed drops off
Stationary squat jumps 2 sets x until you can't go up as explosively as the first few reps
Wednesday:
Dynamic warmup
Stiff-legged calf jumps 2 sets of 15
Double-leg bounding 2 sets of 6
Jumps for max height 3 sets of 4
Friday:
Dynamic warmup
Single-leg speed hops 2 sets of 10 yards
Tuck jumps 2 sets of 10 (don't force it if you cannot explode in the last two or so reps)
You want your movement to be
fluid and
explosive.
For strength, At your age, learning the squat movement would be very beneficial for you later on. I'd suggest to you instead of buying a barbell just right now to sign up to a good gym and learn the technique for the squat and deadlift. The emphasis is on learning the technique. When you can do it flawless, that's when you start slowly adding weight and begin with an actual program.
You want to jump high? Go get what you want, bro.
On free days you should go for a long distance run in the morning, but if you dont have ability to do this its not nessecery. In a days i will contact my light athletic coach , he trains high jumpers and sprinters, and post some more good exercises.
@ Edgaras Pscelovskis - Don't care if you have a 43 inch vert, recommending long distance runs for vert and to "strengthen the legs" automatically makes you lose cred. Can't believe you'd recommend that.