I came to this thread for answers. Unfortunately they are few and far between.
When you have to take Sophia to her apartment: meet her in the garage, walk to the promenade, then talk to her. She will go to her apartment. (It would be nice if this triggered automatically, but that's just my two cents).
I was able to get to the Abandoned Village on the other side of the Graveyard Path by exiting the graveyard after I had given Sophia Strange Mushrooms from the Second Clearing in the Maze. She also needs an empty bottle to but the conncotion/potion in. These can be found by searching at the park (higher perception seems to help). You might need to spend all your energy searching for them.
I am stuck trying to get past the Strange Door in Lily's Room. I was able to build the railcar in the Abandoned Village, but can't travel on it because the game tells me I need to do something at the the mansion. I have no clue what I need to do.
Does anyone know how to get past the Strange Door or how to take the railcar to find Elsa?
EDIT: To ride the railcar, when you get the message "you need to do something back at the mansion" go straightback to the mansion living room. You will have an interaction there that will then allowyou to ride the railcar if you buy the flashlight and go through the catacombs.