EDIT: Below is the problem I had. RVR II uses a different reauthoring method and had no problems. Near as I can tell, it was a problem with Audacity 1.3. Workaround is to convert the Rifftrax MP3 to WAV or AC3 format and use that instead.
So after doing the usual stuff of putting the movie's audio and the Rifftrax into Audacity, I listened for Mike's prompt. "Unpause after The Halcyon Company logo disappears." That's 27 seconds in.
So I delete the introduction, and leave in 27 seconds of silence. Usually when I do this, the movie audio is out of sync by a second or two. It was off by 12 seconds.
I managed to squeeze it in to sync with the 2nd sync line "D'ya think I'm gonna cure your cancer Serena?". That should make everything else fall in to place. It wasn't. The next sync line, and another one around the 55 minute mark, were way off.
Also, everyone sounded really high pitched.
Yes I downloaded the NTSC version. I also tried with the PAL MP3. I couldn't get either to sync up.
My DVD came from Netflix, and has a runtime of 1:54:27.