From what I remember a lot of what your describing is what happens when you try and play a older save on a new version. In particular the characters being invisible and being unable to advance through the story. You do have to be in the right place at the right time to trigger quests though I made a Walkthrough and posted it below if you need to know where to go. There is also 3 bathroom scenes one for each character living in the house/on the farm.