Premiere won't do it, so I had to output from Premiere to a lossless codec. So I've tried Huffyuv and Lagarith, which a bunch of different setting. Everything, at best, produced weird noise every once in a while, even though it looks perfect within Premiere. I finally found a setting that rarely produced noise and only did it in the letterbox section. But the audio had a strange error, where the center channel ran at a higher speed than the rest. So throughout the movie you'd hear high pitched dialog from future scenes. I was able to export a good uncompressed WAV, separately from the movie.
So I tried AGK, which would never keep the audio in sync, and would cut off the first few seconds of black video, further putting the audio out of sync.
I tried Gordian Knott, which would not load the complete AVI. I'm assuming because the file size was too large (37bg for part 1, 27gb for part 2).
Last night I had success with just using VirtualDub to encode Xvid video, and Audacity to convert the audio. When I checked this morning part 1 looked and sounded good. I'm encoding part 2 right now.
The toughest part of all of this is that it takes between 2 and 3 hours to render each part of the movie, and I had to work this week, and had little time in the evening. So I was limited to two or three attempts per day.
-T