I captured the movie once. Vegas captured the video and analog audio, and kept them in sync. At the same time, I captured the PCM audio with my soundcard's software. For some reason, the PCM audio always plays a half-second behind the analog. Anyways, I was able to sync the PCM to the analog audio in Vegas, and then I render the video as MPEG and the PCM audio as an AC3 (after converting it to a Prologic II 5-channel wav.)
"Wouldn't it be easier to just edit the VOB of the TR47 disc to exclude the black space?"
It's not impossible, but it's hard to cut the VOB right where you want it cut. If you can get it right on the scene change, then you can resave the whole file with the added MPEG right in the middle of the split segments. There are many VOB and MPEG merging programs that will do the DOS commands for you. That being said, the resulting transition isn't always very clean, and you may get some visual pixelation or audio drops. As has been said, using the AVI masters results in a much better product, but you do the best with what you've got.