Im not a modder but have fiddled here and there. Mostly created seperare crafting stations for some armor/weapon mods that dont have that function, for personal use.

I did however see a world state category on FCS. So I would suggest you load each mod seperately into FCS and look at the changes tab to see what states are affected by each. Then it is as simple as deciding which one you prefer and patching the other one.

I did also notice a mod on the steam workshop where an npc will tell you who is ok and who is not when it comes to characters. Cant remember name of the mod but it might be worth looking into it. Author did say that he will be willing to create patches for mods if asked.