Just to give you an idea how I did it:
I first thought I would use FCP4.5 (I'm a mac user), but then thought, that it would be a waste to reencode everything just for two little scenes. What I used was MPEGStreamclip to cut and demux the VOBs (and the two AVIs from SciFi). It was a pain in the ass to do it that way, especially only being able to cut at keyframes, but I didn't have to recode a single frame from the DVD material
To convert the AVI from SciFi, I used the MainConcept Coder. Pretty fast and nice quality (also the resizer is better that the one from compressor).
The first episode was very easy, just a cut after the music silenced when Adama thinks Lee is dead (I had to use a few frames more, because the music cue is slightly longer on the DVD), then I hard cut to the end credits from the mini series DVD (I thought about a fade to black, but this way the impact is better IMHO).
Second episode was more complicated. Problem is, the SciFi version used an alternate take at the beginning (reversed angle). So I used two seconds or so from the SciFi version, cut to mini series DVD until the hangar scene when the credits started. Then DVD again in the scene when Baltar sees Six for the first time until the very end. Also I had to use a few seconds of the SciFi versions audio track, again because of the fact the music cue was a little bit to long on the DVD, but I did a upmix to 5.1, so everything stays at 5.1
However, I did not incorporate the audio commentary (I prefer watching the AK as a whole).
No colour correction yet, but video and sound stay in sync, so the next step will be colour matching and authoring it using DVD Studio Pro (maybe I will upload a three minute sample later if anybody is interested how it looks).
For colour correcting I have a question though:
The x0-project used AVISynth to set new white and black levels (link to article). Sadly, there is nothing that powerful on mac. Has anybody a suggestion how I could do that on a mac? AVIdemux offers some tools for colour correcting, but not an option to set new black/white levels....