I'm not a RenPy expert and unfortunately I can't help you with your log analysis. But you can try to write to the developer (
DecentMonkey) in the PM. But in any case, you have an alternative solution to the problem. Start a new game in Ep3, then answer all the questions the game asks you, then you can continue to play. As a result of your answers to questions about the decisions Monica made in episode 2, the game (Ep3 v13) will save the required variables in the new save file and in the persistent file, which will keep your playthrough unique.
The only disadvantage of this solution is that you probably won't save Monica's stats (corruption, decency/bitchiness, amount of money, which, however, can be easily fixed with in-game cheats or entering cheat codes in the developer's console). Plus in the quest log you won't see all the progress your Monica has made within Ep2 v16. But essentially these are cosmetic things that don't affect gameplay and you can always choose this option with "New Game" as a fallback.