That's a huge set of questions - you're looking at a textbook worth of answers there.
A couple of places to start would be to check out Science and Practice of Strength Training by Dr. Z, a decent conceptual biomechanics book (you can go quantitative if you want obviously), and a text encompassing general human and exercise physiology.
Once you have that generally down, you do an analysis of the demands of a sport (biomechanical, physiological, psychological, etc), the time frame, the current condition of the athlete, and how to best go about improving what needs to be improved with the time/equipment available.
The NSCA textbook does a pretty good job explaining how to coach/train an athlete as well, but it doesn't go much into the whys of physics/physiology.
I'm sure others will have some resource suggestions as well, these are just a couple off the top of my head.
Most of the questions you just asked there are totaly dependent on the athletes sport. You have to know their sports inside and out, and understand how the body would best perform in those conditions in order to have a good understanding as to how you should go about training them.