If you want to save the stats of the players, use an event that removes an actor, then inserts another WITHOUT initializing. Initialize puts in the charecter with it's initial stats, and not any that it has gained. If you don't initialize, you don't have to save the stats as variables.
For the multiple stories, just have a switch turn on when one story is completed, then make a condition that something happens when all switches for all stories have been activated.
You can also do that for charecter progress. Once you complete a stage or section of that story for that charecter, turn on a switch that says you completed it.
Making save points would be a better idea in this game than being able to save anywhere, by the sound of it.
If you want it so that the player resumes where they saved, make 3 variables, one that save the chaecter's X, one for Y, and one for Map ID, then have the charecter warp to that spot when you begin the game as that charecter. Make sure you do this for each charecter.