I am going to try the "stitched" video approach in the next week and see how it works for me. And when I say "stitched" I mean exporting the long video into multiple separate SWFs and trying to load them sequentially with scripting.

I have noticed that rather than feeding the source video in to the FLA as one big file, if it's broken down into smaller files and brought in and laid out on the timeline sequentially, if it drifts out of sync in one clip, when it hits a new clip in the time line it seems to regain sync for a little while. I haven't tested enough to see if this works consistently or not, but it might be another thing to look into. I'll be playing with this as well.