One way to simulate your docking rearm, would be to have a dockpoint on your capship in the pods, then have your player approach that point and then map a key to trigger an event with the player-use-ai sexp and a docking order. Then chain it to a has-docked-delay, then rearm the player ship (I think there's a sexp to do that) and repair subsystem dammage, followed by an undock command and then toggle-off the player-use-ai and you're back in the game. Of course, that leaves your wingmen high and dry, since AI is not set up to recognize a capship to have rearming capabilities. It'd likely require some major code changes, which would then render my previous sexp scripting, unneccessary.
As for launching fighters, what you'd want is them to depart out of the tubes, then land in the pods. In FSO, you can't (yet) designate which bay of a ship that a figther will land or take off from. It has been proposed in the past, and I have brought up a means of possibly restricting these actions through scripting using a hypothetical sexp that would descriminate between fighterbay paths by their path name, allowing one to designate wing to arrive from paths bay07, bay08, and bay09 and then depart through paths bay10, bay11, and bay12. These would need to be controllable both from both the ships and wings editors, as well as through sexps, should conditions need to change in-mission.
Later!