Where the times are concerned I would recommend looking at the time it was cut off (4:02/4:03) and the difference in length of songs/silence left on WayTheGirl, I have no way of explaining these abnormalities... If there was a problem when he originally download the midi, it shouldn't have been able to play or it would have played right up until 4:02 and then stopped playing completely. Its also strange that with so many other versions of this song Lun choose this one which is the painstaking length of over 19 minutes (Most other versions of this song is 3-4 minutes long).
The electronic sound that is heard at specific times seems to be constantly at the same part in the song, so that might be more to do with notes being played at the time.