CapableMetal's encode synchs exactly (as far as my eyes and ears can tell me) to msycamore's m2v. I made an AC3 in Aften because Mainconcept choked on the FLAC, but it seems to have come out a bit loud relative to a "proper" 5.1 AC3.
I also OCR'd the 2004 subs and synched them - to see how well they'd work. (Don't mind the quality, this is a test encode)
I swear I remember the video using Helvetica Bold for subs instead of the usual Alternate Gothic...am I misremembering?