Hi Arathel.
When you say "the story file", are you looking at the raw Story.Div file? This is indeed a text version of the entire Story code of the mod, and reverse engineering it into individual goals is possible but seems like a very cumbersome procedure. Diffing two mods to see what exactly each of them did seems even more cumbersome.
If you want to merge two mods, you should look at the individual goals supplied with the mod. When opening your Story editor, the ones specific to the mod have a white background whereas the ones that are inherited from a different mod have a grey one. Goals that exists both in the parent mod and the active mod are shown with a white background, and only the contents of the mod's goals are used.
So the simplest way for me seems to be to, firstly, make sure your compound mod has all the same inheritances at the two mods you're merging, and then copying the goals (respecting their mutual structure) to your new mods. Any goals with different names you can copy as-is. The only issues you should face are if any goal exists in the both mods (in which case you'll need to look at what specifically is happening), or if the mods use the same function or query for some conflicting purposes.
I'm not sure what you mean by "increment Goals down the list"?
Also it may be helpful if you could provide an example of such a conflict.
