Well, the audio is PCM for the PV vobs I have, the usual H!P stuff, so it'll be encoding wave to ac3.
For the muxing, I was going to use vdub mod, and for encoding the video I was going to use Gordian Knot.
My usual audio encoder I use, DBPoweramp, can encode the wave to ac3 for me, but not too sure if it'll give me the 5.1 I want, so I'll just need to check the settings when I encode it.