I unfortunately don't remember anything about pottery, but it is possible to interact with the vase later in the game. Maybe the frame said something about poetry? (because you find the first letter in a poetry bookcase) And the key does not count as one of the six items needed to get a different cutscene. You are missing a pile of clothes. If you need more help, just ask!
The box with the knife disappeared from the game permanently when you picked it up as Haru. I think the box you're supposed to look for is a bit larger, but not as large as the crates leading up to the attic. The box should look like the one in the room with all the photos hanging from the ceiling. Good luck with the rest of the game!