Hey, I'm a pretty intense wrestler so I do tons of body weight conditioning so this might help you out some.
To train for push-ups and sit-ups I suggest doing the exercises and trying to develop a pace. Figure out a method that works for you as well. For push-ups I did 50 in the first minute and some change and then did 10 10 5 with rests in between each 'set' (resting in the up position). For sit-ups, I probably used a pace that was too fast, but it did not matter for me. I would suggest trying to do around 45-50 a minute at an even pace for practice. That method could be applied for push-ups except try doing about 30-40 a minute for practice. Pull-ups get people, but I know how to train up for those (can do 30 complete dead hangs and 50 'sloppy' ones). IF you can do pullups, the trick to improve your number is to do pyramids. For example, do 1 break 2 break 3 break 4 break go all the way to your max and then back down. IF you cannot do pullups work on doing lat pull downs, curls, and reverse curls. Have someone help you out by pushing you up and then you provide resistance to slow your descent as well for practice. Basketball throw is all technique, shuttle is all in the transitions, and the mile is just plain practice doing some quaters, miles, and the occasional 2-4 mile run. I trained for it by running 7 min 3 milers and some quartes at about 1:10. Hope that helps out.