The audio tracks are basically done. I want to test them some more to make sure there aren't any problems, but there isn't really any actual work left to be done on them at this point, assuming I did everything correctly.
Harmy, question: when you tested importing TrueHD into your Bluray authoring software, how did it want this to be done? Did it ask for both the MLP and AC3 files separately, or were they still interleaved when you took them off the source disc? As far as I can make out, when making an MKV file it's okay if the two are on different tracks, but in Bluray format they have to be muxed together, so hopefully the program is capable of combining them, since the Dolby encoder will only provide them as separate files.
The reason for them being combined is for the sake of backwards compatibility: with an HDMI or multichannel analogue connection the lossless audio will be used, while bitstreaming over S/PDIF uses the 'hidden' Dolby Digital track automatically, ensuring that no one will be left without the ability to hear the program. In this way it somewhat resembles the DTS 'core' scheme; the difference being that in Dolby's version the two tracks are unrelated and not dependent on each other. With only one output file instead of two, HD MA is no doubt generally easier to use from an authoring perspective, but I do think that TrueHD will be worth it since there is more Dolby-capable equipment out there. (I'm able to encode in both formats, so if I'm wrong and it doesn't work for some reason, DTS will be provided.)
Darth Real Life requires that I go out of town for the next few days, but once I get back I should be all set to encode and upload everything. This isn't a frivolous journey—it's a conference of audio professionals which is being hosted by one of my teachers, who owns a recording studio and in every way is an extremely knowledgeable and awesome guy. I learned so much stuff from him this past year, and now to get school credit for meeting with his friends in the industry and hearing their views on audio . . . well, for someone like me that's a very exciting prospect. ;)