It does not have to be 16:9 to edit it, who told you that, just keep it the way it is, straight from the retail DVD, you do all your editing that way, then when done let the encoder make it 16:9, you really need to read ADigitalMan's edit Guide, it DOES work, that is how I did my Edits, and I have done a few of them.

I must not be seeing exactly what you are trying to do, but if you are editing Kill Bill with Kill Bill 2, why are you making it 16:9? don't even worry about that until the editing is finished, but you WILL have to make sure that both sources are the same fps, I prefer 23.976 myself, then let the encoder add the flags, as well as the 16:9, and those sample scripts you are showing above, way to cluttered.

So unless there is some other reason why this has to be set to 16:9 now I am not getting, I would not worry about that yet.

reading through some of this some more it is really hard to tell exactly what you are trying to do, you mention a few things, if I was you, I would just slow down a bit, and take 1 thing at a time, especially if this is the first time using avisynth, this would be the best way to approach this, in my opinion.