Body Plugs
Could it be that one reason why those humans who have been freed from the matrix are stronger and faster than the humans who have not been freed be because they are less connected to the matrix as everyone else.
Before Neo was freed from the matrix he was connected to it by many plugs all over his body. After being freed however many but not all were removed by the Neb crew. When they jacked into the matrix themselves they only use one plug which I assume goes into the brain or near to it. Is this the secret to their strength within the matrix?
Second question: considering this, when Neo goes to Machine City and the machines reconnect him to the matrix using the remaining body plugs on him, since he is fully clothed how do the machines know where his remaining body plugs are?