If i understand correctly, You want to save variables to let the game know what the user picked. And also know what path its going and thus show the correct ending?
Truth be told. my game only involves minor paths in the beginning. From where i am now onwards. I stand before that very same problem. Though since i already successfully save and load 4 slots and load ''rooms'' and ''line numbers'' I have no clue why that would not work with more variables. (loading and saving would take a tad longer maybe?) Play my game and save and load it. Youl see it saves what part of the story your in ( Though the room numbers dont say alot to regular players, i might change it to shorts words about where in the game you are ) It shows exactly where you are and all
If your interested and get into DSGM. Feel free to ask me or the community about this ( Though the community of DSGM are alot of young guys. I'm 2nd oldest person there and im 19y old. (if im correct))
I am one of the first that uses this much save and load actions in 1 game. So yeah not to brag about it, but i think i would be your man to explain it for a bit
Good luck with the game! I hope i get this 4MB limit thing solved before you run into things like that! (many backgrounds == alot of space
)