Yida's 3rd scene is available after killing all enemies in the first area (Lampcrop Borderwoods) and going back to the house. However, if you've progressed in the story past a certain point (meeting Headless after the 2nd area) it won't be available anymore. It's definitely still a little buggy to actually get, so I'll look into ways of fixing it in future updates.
For Black Hound you have to bring her a total of 3 diaries.
The first two are found in Lampcrop (the hints.txt file in the game folder should have exact locations.)
Then there are two more in Flooded Colony:
3 is found by exiting out the northwest part of one of the southern areas. (It's the map with a large park filled with blue flowers.)
4. Is found on a box in the north-eastern part of the area. 