You need Womble and DVD-Lab Pro at a minimum. Make www.videohelp.com your other favorite site (I've been there for years but never got serious about editing before the SW DVDs came out and disappointed me). The soundtrack will stay in 5.1 on the condition that all sources are in 5.1 and that you don't manipulate it beyond straight cuts. I've found that you can cut the audio in a different place from the video and often "hide" your cuts that way. Great for those moments where you lose a soft wipe. Cue the transition music a bit before the video cut and you've actually got a pretty nice transition.
DE, I guess I do know what your forthcoming change is. Not what I was thinking though. I imagined a real and total heresy like creating a visual of Obi-Wan's spirit leaving his body as he was cut down. Which, heretical though it might be, would be a darn fun project for somebody (not me) to take on.
I look forward to this whole thing when you're done with it.