Soniram
These are the joys of "sandbox" with choice of relationships, the more you will advance in your game, the more your trigger conditions will be broken according to the choices of each one.
But I agree with you that the hint system is still a mess for some sections.
Yet I'm not a boring player, I take everyone.
The clues for the characters have really improved since the beginning, I haven't had any more problems, although I didn't try to be boring and avoid certain characters.
Besides, in advice, you should put the secondary characters back in the part book on another dedicated page for them, as at the beginning, it's easier to see what it takes to trigger their quests.
The one that I still find chaotic personally is the main story part (Threads)
Sometimes it is clearly indicated sometimes not.
Sometimes we look for how to trigger it, other times it happens all by itself without us knowing it.
By the way, I still have the problem with Katira (goblin) with the quest sequence which begins with the scene in the store where she breaks everything and throws her clothes away (I restarted a game several times and I always had this bug)
On this part, I have already finished the quest 3 times and it repeats itself again.
Anyway, good luck to you, because I really like your game and I can't wait to get to the main storyline and move forward with the relationships!