Say what?!? PCM is mandatory for DVD players, since DVDs are required to have either a PCM or DD soundtrack. Are you sure your PCM file was good? Did you try playing the PCM file on a different disc?
"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."
What if the "spot" is from the laserdisc material itself?