This is less a question about Morrowind Crafting scripts and more a question about moving scripted objects from one mod to another.
What happens is this: You copy the object into your mod and the object data (including information on which script is attached) is added to your mod. But the script itself isn't part of the object definition. Only a pointer to the script is part of the definition. If you don't also edit the script (open it in the script editor and save it again) the script itself isn't added. As long as you have the original mod loaded when you're editing your mod, everything will be fine, because the construction set will be able to find the script. But... the moment you edit your mod without the original mod loaded, the CS can't find the script that the object definition points to, so it deletes the pointer to avoid errors. After that, the object is no longer scripted.
The simple solution is just to add the scripts to your mod by editing them while MC is open, and then assign them where they belong. After that, the load order won't be an issue. Personally, I recommend that modders do as much as they can to make their mods load order independent. There are times when having a specific load order is necessary. But this isn't really one of those times. It's more user friendly if the end user doesn't need to worry about things like load order.
Of course, if you saved the game with this mod active, you'll have a dirty save. Even adding the scripts to the objects won't make them work because the un-scripted version will be in your save game which is loaded last and will override any changes you make to the mod.