Q: What do the colors mean? A: The colors indicate different melodic lines in the piece. The part for pedal (the lowest part) is always violet, and there is one stop (starting at about 4:55) that is always blue, but the rest of the colors just indicate different melodic strands (and don't correspond in a consistent way to anything in the score).
Q: What instrument is this? A: The sound comes from two Ahlborn-Galanti organ modules. Most of the stops come from the A-G Silbermann module, but the 32-foot pedal stops and the contrasting stop (the one at 4:55) come from the A-G Romantic module.
Q: What are the gray bars? A: The gray bars show the theme of the passacaglia (the first part of which is also the main subject of the fugue). The colored bars show the note duration of the performance, but the grey bars (which is bigger so that you can see it when it's behind the performed notes) show the duration of the notated version of the theme in its standard form (which is often very different from how it appears in the piece at a given point).