that might be part of your problem, going to bed is part of advancing quests too. Most of the bugs in the game IMO, are because this is a VN pretending to be a Sandbox, there are many points that the game expects you to hit in a specific order but the Dev has failed to put proper blocks to keep you on the right track, so sometimes you are trapped in a situation the game can't handle.I don't focus on any track, i just try make all i can in one day, to avoid go home/bed, so if i can do like, 6 tasks in one morning, i will do it, then i will try do the same next times, some times it just spend all day and i forget who started what quest...
It's tough to advise you because you can't even gauge the sequence by the order of the hints since some are revealed way before you can do anything about them.
The only real thing is to save often and across several slots. and save before you enter special locations.