The re-encode went smoothly and I am very impressed with the results. It now plays without so much as a stutter in all media players I throw at it, which I take as a good sign. I haven't burned it to BD-R yet and tried that, but BD compatibility is definitely a goal. I will verify this before I'm finished.

I'm in the process of uploading a clip, please PM me for the link. It is a BIG file for such a short clip, because it's a full-resolution M2TS, with all audio and sub streams too. That way, you can see the actual video quality, and also how I handled the cut on alternate tracks and subs. MPC is able to switch audio and video streams through the "filter" menu, FWIW.

As far as things left to do, there's a better Japanese and commentary track I'd like to have (in fact, the current Japanese track is so bad I probably will not include it in the final unless I get a mono replacement), and I'm toying with the idea of adding a German subtitle track because that's something I feel I can manage. A Japanese-back-to-English track would be great too, and I may just know a couple of people who can fill in any gaps.