I mentioned a different counter since sufficient bed and shelter can be unobtainable at times (Especially when you add 4+ settlers in one night), the bad pathfinder can invalidate the run for cover, and it simply feels like owls are too weak in their current form. Corn would work well as a third food source, reducing the pressure on traps, which often eat into the building resources. I suggested disabling owls since it would allow me to move and do things freely at night, which would help significantly (Unless you are not supposed to gather resources and build things at night.). Danger should be telegraphed simply as a notice of who, how, why, and sometimes where. For references on threats, I recommend the Rebuild series and Hive Time (You easily could go down the semi-educational route Hive Time did). No Man's Sky's settlements is a great reference for settlement management (Especially in 3D games like this) and Minecraft continues to be a good source of things done wrong and right for sandbox games. (Your owls resemble phantoms, which that community considers a nuisance). A few more things I remembered, I would be careful with linear progression in this game, since players may use it to optimize the fun out of the game. I recommend keeping stone and wood as separate upgrade trees, as a player who wants to switch from one material to another can replace the walls. This fixes another issue I noticed: upgrades lose resources. If you are willing to deal with a game with a complicated relationship with SFWness, Cataclysm: Dark Days Ahead is an excellent resource. That said, I would also be careful with open progression, as some players flounder when guidance and objectives are absent. While I do not know of something on balancing linear aspects, acgaudette (who is on itch) wrote several blog posts on balancing openness and sticking to your level of abstraction. Lastly, two things with construction. Firstly, built objects should not cost the full amount of resources until it is built. You should allow partial construction (The most common) or block construction until all resources are present. In addition, a proper planning mode would be very useful and help keep the settlers from bottlenecking on their auto buildings.
Notify me if you want me to put the suggestions on separate lines.