As for removing the 3:2 pulldown (i.e. Inverse telecine or IVTC) it was the first thing that was done to bring it back to the original 24 progressive frames. It was a bitch too, as there are errors on the laserdisc in some scenes where the 3:2 gets out of whack, so has to be manually adjusted.
Ugh, I know exactly what you're talking about. I especially enjoyed the bit in Jedi when the Emperor is shocking Luke and the 3:2 switches back and forth twice in about 5 seconds. I had to re-encode an entire disc because of that one...
Sounds like you guys are doing a heckuvalot of extra work on these. Here's hoping I can dump even my own version in not-too-distant-future...