If you haven't already gone about figuring this out for yourself, I'd look at what others have done, XP and/or VXA. Basically you are going to have to rewrite a lot of the default methods and add new variables to be saved. Game_Party for sure will have to be modified significantly.
All you really have to do is sit down with a pencil and paper, see how the default system works, and figure out what is the most practical way to solving it. Be a true programmer! Problem Solve on your own!
(I have over 50 pages of notes and ideas just for my Advance Wars Engine alone. Had to buy another notebook specifically for it.)