Don't focus so much on the basketball throw and shuttle run. Instead put more emphasis on sit ups, pushups, run, and pullups.
For pullups I suggest the Armstrong pullup plan (look it up). It was created by an officer in the USMC. Pretty much everybody training for the Marine PFT uses it. It got me to 13 pullups in about 8 weeks, and I used to not be able to do one. I've now switched to a program called recon ron to get me the final 7 pullups so I can max out on the Marine PFT.
For pushups what I did was start a few sets of pushups in a decreasing rep scheme. Initially I started off at 20, next set 15, next set 10, next set 5. Every week I increase it by 5 pushups. If I struggle to do 5 more for that week, I'll repeat the last week. So for me by now it looks something like 40, 35, 30, 25, 20, 15, 10 and 5.
For situps I just add core excercises whenever I'm at the gym. Sometimes its leg raises, weighted situps, crunches, etc. I don't really have a set excercise for situps, I just do them.
There's a ton out there for the mile run. One program you could do is this. Run 3 times a week. Monday do a 3 mile run. This will be for stamina. Wed. do 3 sets of a one mile run, this will be so you can get used to the mile. Friday will be sprints. This will focus on speed.
Hope this gave you some guidelines to work with. Good luck! And don't forget the key isn't necessarily what plan you use, but rather dedication to a plan.