When I started to design the game, I decided to test Ren'py engine's limits by trying to make a VN as interactive and complex as possible. As my final, long lasting goal is developing mainstream indie games, I envisioned different ways to finish quests, getting different outcomes and by giving freedom of chioce and movement to the player I aimed for a natural feeling for gameplay.
At this point, I feel that for a lone developer, because of the initial rather large scope of this idea, testing is where I failed to make it happen. As I know what the most sensible way of playing order is, I don't encounter these bugs that you're experiencing. Maybe some Ren'py weirdness is putting more kindlings to the fire as I saw some inconsistent bugs.
Anyway that's the nature of the beast that I tried to tame and failed at that. My new course of action will be overhauling the game. I'm thinking on preserving the core, but instead of giving open world and freedom of event orders, I'll dictate players' next actions one by one. I think this is the most sensible way to do it as I often find myself trying to get to the juicy scenes in other VN games. Admittedly it can get annoying to overwork your way to the H scenes in an erotic game.
I'm not disheartened or dissapointed as it was a very valuable experience for me to try to make a Ren'py game of this scope as my first Ren'py game. And in some way I've shown a prototype of the final product to you.
I'm sorry for your grindy experience and thankful for your sympathetic approach to the art and story of the game. Next update will be a general overhaul and will hopefully produce the first uninterrupted experience of the game. It's world and story won't suffer anything from it, only gameplay will be much more linear than this one. As the code will change significantly, your saves won't be compatible unfortunately. But on the bright side, progress will be much easier as your decisions won't be any hit or miss anymore.
Thank you and hopefully see you in not so distant future. Journey to Bliss will prevail!