Never noticed the DVD omission...how many tweaks and edits are there in Leone video editions? ;) Good luck with your edit.
After direct comparison of the 1993 box set and 1998 LD and 1998 DVD, I'm almost 100% sure that the overall source is the same. The damage marks are in the same places, albeit a bit cleaned up on the 1998 version along with less video noise. (Like the Fistful print was cleaned up for the 1st DVD vs. the Laserdisc) The mono audio is the exact same track with the same dropouts in the same places.
Damage example to check is lines running through the print when Tuco staggers back into town from being abandoned in the desert.
Audio dropout example to check are blips in the first master shot of the final duel, in the rising trumpets.
Can you say where the reel change marks are? I didn't see any, but am only spot checking the '93 disc. It also doesn't seem to be cropped like many say the regular letterbox version was.
What I'd really like to do is restore the International version and then the Italian release version with the current HD versions, which would only leave the grotto scene (for an extra or to make the premiere version), "Sorry Tuco", English final line shot and International edit of the Tuco torture sequence to be sourced from the dnr MGM source.