I could be mistaken about you missing some of the duel shots. I was going shot-by-shot in order and I noticed that the album didn't match the film. This could just be because there is a shot or two that you listed out of order, as this happened at least once earlier. Rather than figure it all out, I just decided to stop using the album and just catalog each shot myself using the film. I ran into this with the prison shoot-out too but I think in that case I was just confusing myself and had to do lots of album-to-film comparisons as I went to make sure I was on the right page.
With the trench run, I really have no idea when it comes to replacing the background for the cockpits. It's too hard to tell because the video we have is so bad, looking for signs like matte lines is such fine work that it often is difficult to see in video from the 1990s. It doesn't help that I was using Puggos 16mm either. I guess what you could do is look at each shot until you can find some clue you can use as a reference, like a transparency or a matte line around the actor, then go check that against the SE and see if that reference clue is still present, and if it's not then it means it's a recomp. You can sometimes tell if they haven't recomped because the colour of the background is a little off, the Death Star sometimes prints as a mild blue or purple and the space and stars sometimes print blue.
It's such a headache I just listed that one shot of Luke that you did and called it a day. :p If more are ever identified I will add them.
I also noticed the Kenobi tractor beam matte was not listed as a re-comp. I wasn't watching the SE, but I thought that was re-done. Or did the black crush just make it match better?
Here's a question: is there a single visual effects shot in the film that isn't changed?? When I was going through the list the only ones that I noticed were missing was the "Here they come" scene and a couple of cockpit point of views. You don't list the shot of the SD going towards the DS, but I don't remember seeing any matte lines on that in SE, but maybe I'm just not remembering it correctly. It would be interesting now to catalog the shots that have not been re-comped or touched in any way. There's probably only a handful of them! This would be an interesting analysis to use in that you can scientifically say that 90% of the Oscar-winning visual effects have been removed (and yes--to me, the composite is the effect; a model against bluescreen is not the visual effect, anyone can film that, it was the way they were put together that was pioneering).