Since there's interest growing in this, here's my alignment/clean-up script. I'm currently re-working the upscale aspect of the script, but this is the basis that underpins it, and I haven't altered it since last year (and probably won't). You need to crop the right-hand side of the final product. I use that script to create uncompressed AVI files of the scenes I need, and then load the scenes into the upscale script.

Also, I have worked out how to handle the bridge scene. Labour-intensive, but it will work. :)