In order to achieve a rot spot free transfer, there is an AVIsynth filter called "TOOT" that will check three separate sources of video pixel by pixel and average the two most similar. So, for instance if I make three captures from three different ANH LD's and on one frame one has a rot spot and the other two don't, the output video will be without that spot. Using this method, I should be able to produce a transfer that is rid of all rot spots.
Got a link for that TOOT filter (google's got nuthin)? I'd like to test it out on some of my own captures.