It will never sync up correctly with the KCCI version (too bad, since that's the best one) because of the commercials and the bizarre opening crawl*. To sync it up with the Google mp4 is very easy though. The movie commentary begins 2 minutes and 36 seconds into the RiffTrax file. Just use Womble to offset the beginning of the video and export it. Hell, I watched the movie with the commentary in Womble's preview window. No burning required! Not that you could ever put it up here, of course.

*Well, I suppose you could edit out the commercial portions of the RiffTrax files (and any references to them) and try to line it up with the KCCI version, but editing out just the right number of frames with the fade-ins and fade-outs to keep it perfectly in sync will be a bitch. On a side note, where the Hell did that Godawful title crawl come from? Please tell me it was fan made.