It might be very difficult to try and restore the accurate lightsabers while still using the 2004 DVD footage for the scene without it looking like it's been altered in some way. Probably better to just replace the entire duel (from the time the lightsabers are first activated by Vader and Obi-Wan to the end when the blast doors close in front of Vader), either with the GOUT footage or perhaps use the 97 SE video for the entire scene.

This is just like the situation with Jabba's palace in Return of the Jedi, where the entire SE-changed scene needs to be completely replaced with the correct GOUT footage in order to restore the scene to the way it should be.

If the lightsaber appearance in the duel in the 97 SE is accurate to the GOUT, then the 97 SE video will do very nicely. :) Max_Rebo is currently working on putting together the highest quality 97 SE DVD set he can. He has very high quality 97 SE video that is even above NTSC DVD resolution, the TB video capture quality is great. This video is in PAL format, but after it's been adjusted to the correct NTSC video frame rate and the aspect ratio has been adjusted to match the 2004 DVD (which I think Max_Rebo may have already done by now), it should drop in perfectly and match up exactly with the 2004 DVD video from before and after the duel. Perhaps Max_Rebo can supply the video you need for the duel (as well as others scenes for Star Wars and the rest of the trilogy you are working on). You can read about his project in the thread below. :)

http://originaltrilogy.com/forum/topic.cfm/Max-Rebos-97-SE-superset-preservation/topic/9031/