Hmm... I think the Vader scene does exist aside from within the master of the Holiday Special; after all, it was only full screen there. I'm glad to hear that there's HD deleted scenes; those should prove great fodder for fan edits...
I think this will be the basis for the 3D version that will come out in theatres. I don't think LFL will consider going back to a rescan and manually redoing the 2004 changes. I'm really hoping that LFL did honestly bother to make this version look nice; the digitalbits review does look promising and I thoroughly trust that site, so my hopes are somewhat up.
The one thing that amazes me is how they fixed the Humdinger because of public reaction. I guess LFL isn't yet at the point to completely ignore the public.