1. the cut before "she would undoubtably be it's mother" is intentional - "it" does not necessarily mean "the Matrix" or "program".
2. the edit involving th Deus ex Machina was also intentional and involves the nature of the Real World in relation to the Matrix.
3. as for the speakers, I had debated using a different piece of music, but the 5.1 mix of the films (which I used to create the audio mix) didn't allow me to effectively switch out the soundtrack without losing the sound FXs of the scene.