The dev just responded to the thread comments about how to move on ... Basic plan is, install a "clean" version of the game and load your last modded save.
Assuming it works, you then can resave that, then play out the rest of the chapter without the mod (hopefully you're really close to the end or you remember your choices) and let it finish so the persistent file needed to start the new game properly is created.
Then, after MM has made the S2 mod, install and start the game (that said, it may be safer to start a "clean" version of S2, start the game so it definitely picks up the info, then save quickly and wait for the mod to continue ...)