The trick to modding is to create a modfolder.
Inside of c:\program files\se4 there is data, pictures, etc.
Create a new folder, called "My mod", say.
Then for any files you want to change, place them inside the "my mod" folder as if it were the SE4 folder.
So, you would have c:\prog files\se4\mymod\data\components.txt
of c:\prog files\se4\mymod\pictures\combat\torps.bmp
and so on.
Then your original files are pristine and fresh, no worries.
In order to use your mod, edit the path.txt (in the se4 folder with the SE4.exe), and change the "path := none" to "path := mymod"
Presto changeo, SE4 starts using your mod, and any files it dosen't find, it will look in the defaults for.
This also lets you install a whole host of mods, and flip between 'em easy.
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As for restoring the original files:
The Unmod.zip will get you what you need