Seems like the only way to feasibly do this would be to have something similar to the gimp image registration plugin(it automatically resizes, scales, and aligns similar images according to a reference image), but I don't know of anything like it in avisynth. Anybody know of something like this?

I'm not really interested in overlaying the pan & scan versions with the widescreen but I would like to overlay the jsc, gout, and se using the jsc chroma information to be able to mix and match the gout and se dvd's without having to worry about color correction. Unfortunately the cropping on each edition is different so the only way I can imagine to do this would be to register the images together before transfering the chroma.