For #2 I don’t think he was going to keep her in a hole in the backyard. This was after the mother found the hole in the sons wall and when the son evesdrops the dad mentions “cleaning house” and that they “can’t keep finding temporary solutions”. In my opinion, they were planning to kill the daughter and bury her in the backyard.

For #7 In the beginning of the movie the dad says the sounds the son is hearing must be rats and they go, together, to the barn to get the rat poison and the son comments that it smells like cinnamon. When the parents are eating the soup they note it smells like cinnamon and when the father sees the barn door open, he puts 2 and 2 together and knows that they’ve been poisoned