First up though--starfields, engine effects and blasters. On the 2004 DVD the starship engines don't have a glow in many shots---see the shot of the Falcon you posted and the Tantive IV. If you really want to be anal these should be colored, but with the method you are using that might mean hand-rotoscoping of some kind (you could possibly overlay them from another source--the GOUT unfortunately has aliasing issues so if you use that source to overlay then you have to correct that first). Also be careful about the missing frames from the two death star officers shot, people tend to forget about those changes (I think theres also an extra shot from the prison control room shootout omitted in the SE but I can't be sure). And of course the lightsabers--preserving the original lightsabers will be tricky. Good luck with that!
Color-wise its good that you are using the GOUT. IMO its the best reference for original colouring--theres little to no color issues beyond maybe a bit of a bump of the contrast and saturation, but I think that simply makes up for the small amount of fading done by the duplication and aging of the film. The black levels are not strong though but simply in terms of coloring its one of the best references to use IMO.