Right at the beginning, when it switches from the heart monitor to the Koy footage, you delay the scene change just a second, or make it fade quickly, to line up with the cresendo of the opening guitar/drums intro. I would also recommend using the IRE fullscreen (not cropped widescreen) version of Koyaanisqatsi for the video footage (search these forums for more info). And finally, I would (personally) use less stills of the band, and more Koy. These are of course, just what I would do, but I just thought I would share some of my ideas.
Overall though, it's a pretty cool idea, and I wish I would have thought of it first, with other music
. Definitely keep us updated on the DVD!