Well, I checked my applyweb account for Stanford today. It says they have received all my documents, test scores and LORs. But my application status still shows incomplete.
I think it's probably because I sent a hard copy of my transcripts to the Physics department mailing address instead of Applied Physics. I sent them around a month before the deadline and at that time I thought I would be applying to the physics department! [The addresses are different]
Should I send them again given how late it is? Is is possible that the physics department could forward my transcripts to the applied physics department? They do have a unofficial copy of my transcript uploaded with the application.