I just checked the "topical" scenes that have been retouched and I have to say, it's pretty good. Audio tracks are in synch too... all seems fine. Thanks everyone for your help during these difficult encoding times. It's not over yet for me though, I still have to work on the subtitles and I'm probably forgetting many other things. If I can't create any menu then I have to find out a way to make a playlist so that a short clip can play before and after the actual film.
As for the MKV, from the start I never planned a digital release because I'm paranoid that my work would end up on public torrent websites. I prefer the burden of uploading 23GB in parts for forum members, makes me sleep better at night. We will see about a lower resolution MKV for the simpler curiosity of checking the film with my tweaks.