When you say copy and install, do you mean copy the mod files or copy the C3C files before adding the mod to it? I'm not sure that copying the mod makes any sense -- after all, those are the files I'm trying to install! Besides, I have the .rar as a backup if needed.
But then again, copying the C3C files doesn't make any sense, either -- installing the mod means adding a new subfolder to the civ3/Conquests/Scenarios (or civ3/Conquests/Conquests) folder. I'm not overwriting any files by doing that, so there's no need to make a backup.
As for running a diff on the mod files...sure, I could do that, but what do I compare them to? Obviously I don't have all the files in the right places, but since I don't have an encyclopedic knowledge of the mod, I have no way of knowing what's wrong or what's missing ... until the AoII save crashes the game.