I have question that I do not think has been addressed yet. I understand that when an EMP fires, it destroys anything electronically active. Does this include the EMP device itself? I would assume so, since it has to be electonically active to create the EMP.
My theory on why Neo was physically jacked into the Matrix after his rescue from the train station: The train goes between the machine world and the Matrix, right? So Neo had to go from the train station into the Matrix and then out by typical means. I am sure that Morpheus and Trinity called...