I'm not going to write out the script for you because it's important to figure out what each little sexp does on your own. But here it is in laymans terms. Besides that, I just woke up and couldn't tell you what color my shirt is.
#1. Okay... you know when you're editing ships and it has the arrive/depart windows? In the depart window, you need to set up a condition (all enemy fighters destroyed? Player has accomplished a certain goal? Whatever it is...), with the result that the shuttle will depart. Set up the depart info for a docking bay, and select the capital ship you want it to dock on. When the condition is met in-game, the shuttle will head for the carrier. Getting it to re-launch? Create a new shuttle, with a point somewhere in space that you want it to launch to (make the name very similar or with an extra space or something, because you can't have two ships with the same name), and in the arrival window, put a delay of 120 seconds, and the arrival condition (the window on the bottom) is the "when-departed" with the old shuttle.
#2. Script an event that will end the mission when the distance between Alpha 1 and ship subsystem (choose a docking bay) is less than 60. (You can use another number, but I find 60 is a good distance).
#3. Objectives are just events that are "accomplished" when whatever sexp you set up becomes true. The details depend on the mission. Waypoints... do you mean autopilot? Until you get really deep in, I suggest you just use simple time compression autopilot. I don't have enough time to write it out for you right now... have to feed the kid breakfast... but I'll come back and give you an example. I'll write this one out for you because autopilot drove me @#$%ing insane for two weeks.