For the high quality file, encode to 10 bit 4:2:2 HD for video, and 16bit/48Khz FLAC (shaped dither) for the audio tracks. That level of quality would be professional level/optimal for future fan edits, show-able on large screens, and would make a 50GB MKV justifiable.
Please do not waste time and data encoding the audio to DTSMA as it's efficiency is somewhat below FLAC, or rendering to anything higher than 16bit/48Khz as that'd be sheer waste.