I've re-muxed everything and developed a strange error. If I preview in PowerDVD on my drive, the scene with R2 and 3PO talking with Bib Fortuna stutters (like it is freezing on keyframes or something like that). However, if I view the VOB file in Windows Media, the scene plays fine. A curious anomaly. I think I'll take my chances on a burn. I get the feeling the data is just fine, and will read just fine if unfragmented on a silver platter.
I changed the 2.0 track to PCM. Because I had to convert to PCM due to my crossfading technique, I didn't want to lose any more data by recompressing. It fits on the DL disc, so I just left it PCM. I even normalized the track, so it should be a bit louder than the 5.1 mix.
One movie down, one to go!