I haven't tracked them, and I don't have the time on my hands to go through the game again to make a note of the vague ones, sorry. This was just my general impression the last few times I tried to play without the walkthrough.
What about the content that's not referenced in the quest logs (and I think there's a lot of it), I'm curious how do you approach that without the walkthrough?
Edit: Just gave it a try with the the current version. Tried following Penny's quest for rebuilding the farm and the instructions were actually good until I got to the point where the MC is supposed to be inspecting the mill with Penny, and I got stuck there. I first cleared the area with the mill, went to Penny, the MC still says he hasn't checked the area. Went back and cleared the area to the west of the mill, as well. Same thing. Let's try assigning mercenaries to the area, same thing. So is this a bug, do I need to try something else, or is this the end of the current implementation (quest log doesn't say it, it just says I need to inspect the mill)? Who knows? That's why I usually wait for the walkthrough. But that's fine for me, as long as there a walkthough update coming, I'm good.
