Thank you so much guys for helping out with this.
Good idea about the 2004 SE. I'll probably try to synch the 97 SE completely to that, since it would make DJ's audio synch job a bit easier since we have multiple audio tracks. He could just synch them to the 2004 SE's, with the exception of ROTJ like you say about the Naboo shot, which have to be cut.
50193 - close-up on Luke listening after Ben says "...it binds the galaxy together." May not be exactly this frame as its difficult to tell but certainly a frame is missing from this shot. Middle of reel 2.
I compared it to the GOUT and it looks like the missing frame should have been the very first one of that shot.
Towards the end of reel 3 (reel 4 begins at 90295).
There's an unknown frame missing there? I guess I could pinpoint it once I have it synched to the 2004 SE.
32645 - General Rieekan "prepare for ground assault" (actually around this point, I have been unable to pinpoint the exact frame as there is very little movement where the frame is missing; somewhere just before the officer he is talking to nods, I duplicated this frame in my synch source).
The frame missing should be between 32732-32733. (I have the SW title appearing at 711 now so it should be correct.)
We'll probably use mvflowfps to recreate that frame. (Part of avisynth package mvtools)