actually, i think that the mirror was an allusion to "Alice in wonderland", as Neo must go 'through' the mirror to see the truth. It also gives Neo an example to think about as Morpheus tells him about Dreaming/Awakeness. The wires that are connected to Neo, like in arms, legs, back, are put there by the machines, keeping the human 'hard-wired' into the Matrix, so they cannot be just taken out, they have to be released. I'm not exactly sure what the wires are for, unless they are used to bring in oxygen and nutrients, take out CO2 and waste products, and to allow the machines a way to recover the energy they need to survive.