Where did the box go?

First question I'll attempt at answering. The last time I saw Mulholland Drive was in the theatre, however, your wording is quite useful, so I'll do my best to provide some type of insight. If Betty & Rita go inside the box, outside of the multiple puns that notion can be viewed at within the context of the movie aside ("Have you done this before? [I believe Betty asks] Rita: "I don't know?")

So they go in the box, then it shows the box for a long time (clearly gestation implication/transformation/transference/ [ever see the movie Persona?] some moth/butterfly chaos occuring by the long time lapse on the box)

Now the somewhat subjective POV of Aunt Ruth and the room (womb? cocoon?) Your wording of:

...camera slowly pans up to Aunt Ruth entering the room, and looking around confused. From her point of view the camera examines the room...

Are you saying at this point the camera is representing the box and it pans up to aunt ruth? if it does that are you also saying there's an edit that switches to aunt ruth's pov of view? so, according to your wording the sequence goes:

1. pan up to aunt ruth
2. from ruth's pov

suggesting an edit, which could potentially mean a few of the following.

After the metamorphosis in the box,

1. first off either the POV is aunt ruth's or it's the spirit of the whomever came out of the box. since i don't remember the specifics of the movie super well, i can only surmise that the box in mulholland drive has to do with transformation. i believe it's blue right? the key and the box are both blue, in lost highway inside the jail cell there are electric blue flashes in the transition between the two characters. also a transition without an exit is depicted here. you'll also want to read this in connection with the youtube clip to truly understand some of Lynch's visua cues (sparks always mean transformations of some sort all the way back to Eraserhead maybe even the Grandmother etc alphabet, six men "getting" {transformation) sick{look it up) here's the youtube footnote. so i can only figure that with all the character dualism of projected and actual, whoever is the POV, is whoever stayed in the box. however if when panning up from box to ruth the pov transferred from box to ruth, this in and of itself could be a process of determining, also, in and of itself.

I'll have to rewatch that scene and then potentially edit this response. Hopefully it provides larger questions to your question. ;]

Next! half kidding.

Also, in the episode of Twin Peaks called Miss Twin Peaks, there's a scene at approximately the 25minute mark involving a vice, a chrome box and yes, a key.