The glass box, and what attacked the couple?
I'm new, not sure if it's OK to refer to a later episode--?---
At this excellent Twin Peaks Wiki, it's explained that "The Experiment" - as this character is listed in the credits, is seen again in episode 8. I'll leave the link for you to read the rest of the info, so I won't be posting a spoiler about episode 8 if you haven't seen it.
Can't be Laura Palmer, she was born as a symbol of the good side ( remember, the golden orb that the giant and the fat lady revealed and send to the world, as a response to Bob's orb from the atomic bomb ??)
Yes, indeed - You're correct, it can't be Laura Palmer. People who theorized about her being Laura earlier on this thread were writing before episode 8 aired. As per my previous reply, the woman/thing from the box is The Experiment, as credited in ep 8.
Im watching TP again and Im sure the murderous aparition is the Arm, the tree, because it talks to Cooper and tells him to go certain point, cooper watches Bob driving but cant get out so the floor sends cooper to the glass box, and the Arm gets angry and transforms in that murderous spirit, follows Cooper to the glass box. In a previous scene you can see Bob showing the entity to the woman he killed in the bed in a hotel.