OK, I've just tried to make my first ever Rifftrax DVD (300) following your guide, and I'm 90% happy with the results, but I do have some problems with the audio. When I play the disk, the audio from the original movie keeps "breaking up" every few seconds, particularly on especially loud noises (like the thunder at the beginning of the movie). The audio is also slightly out of sync with the video--just enough that the voices don't exactly match up. Also, the voices of the riffers are all pitched very high--they don't sound at all like their actual voices.
Could this be a result of overcompression?
I think the problems are probably with Audacity, which I confess I had some problems with. I can already tell that it takes some practice to get things synched perfectly. One thing I noticed was that the "Project Rate" in the lower left corner kept changing back from 48000 to the original setting. I changed it every time I noticed, but it might not have been set at 48000 when I exported the combined file.
Comments and suggestions welcome--I guess I shouldn't expect the first time to be perfect!