I was exactly the same until yesterday, I manually played through every (or so I thought) combination and created saves for them. Then I encountered my Cathy issue - I’d played each Cathy outcome in the past, but found that the Cathy outcome that I needed was not saved in a path that I needed to trigger the scene in Episode 10. This left me with two choices - mod a path with the console or create a new save from starting afresh from Episode 1.Yeah... I never play with mods (this game, though I've remade some routes following PDF walkthroughs... I've played many other games with walkthrough mods -- and I'm not blaming anyone who does this for BaDIK; I just don't feel it's necessary for me in this game), but I've cheated to correct things I've done wrong in the past. Since I never did anything the game doesn't allow, I'm safe and my games never crashed.
And what of the future - taking mushrooms or not causes the party in episode 10 to play quite differently but is that just confined to episode 10 or will it have consequences in episode 13? For example, if you take the mushrooms there is a more extensive interaction with Sally - could it be in a later episode you have a chance of a scene with Sally depending on whether you took mushrooms or not back in Episodes 10.
The number of paths and sub-paths is fanning out (as you would expect) making it more and more difficult to cover every single permutation through normal play.