You're right about that, a lot of work has been put into providing more direction for the player. It's a bit tough to balance as the game is meant to be open-ended enough for players to embark on any side-quest they want, but it runs the risk of being too tricky as you said. It's something I will have hopefully remedied in the full version.
As a hint, that area you are speaking of doesn't serve much purpose in the demo right now aside from being a funny little side area, though it serves a greater purpose in the full game. If you're having trouble completing the second thread, I'd suggest to not dispose of the NPC that helps you get access to said room.
Glad to hear you liked it in spite of its flaws. Cheers.