I appreciate all of the input about the rot/dropouts. Maybe trying to average out several different sets will not yield better results. I think I'll just leave it like it is.

I was thinking I would like to make a blu-ray out of this with a simple menu and encode the movie with as high a bitrate as possible. If there is interest I can put it up for those who would want it when it's finished. It would be pretty barebones. Just a toot, an IVTC and possibly a levels/saturation tweak.

Can anybody recommend software/codecs/settings?