Well, the method I've mentioned makes exactly what I have written, simply takes the GOUT video as the base layer, and puts over this layer the same video from the 2004 release with black being transparent. That's why the code doesn't work.
Both Layer and ColorKeyMask expect a clip as their parameter, and not an avs script, so you should have it ALL in one script, and you should start it with for example
GOUT = mpeg2source("path_to_GOUT_clip.d2v")
SE = mpeg2source("path_to_SE_clip.d2v")
GOUT = GOUT.Trim(..., ...) #the start and end frames if you want to do it only with one scene
SE = SE.Trim(... , ...) #the same
GOUT = Crop(... , ... , ... , ...).Lanczos4Resize(720, ...) # crop it and resize, the numbers are depending on the format you're using (NTSC / PAL)
#and later use
Layer(GOUT, ColorKeyMask(SE, $000000, 10), "add", 255, 0, 0)
That's one method. If you don't wanna do it this way, tellan wrote a couple of month ago a different method on chroma keying in his "Lancer project" thread. Maybe it's worth reading. 
I personally want to have it done before Christmas 
How many versions of this movie are there actually ?