I recommend git. GitHub Desktop isn't terrible to use with it either although it's pretty basic.
- Start your repo from the base game files, then convert them all to UTF-8 BOM.
- New branch from base, apply patch converted to UTF-8 BOM.
- New branch for each mod from patch, apply the mod converted to UTF-8 BOM.
So your branches should have: base-data, patch, translation, mod-1, mod-2, etc. You can also easily see all changes made by a mod to the base game files.
The reason for converting to UTF-8 BOM is so git works properly; the regular files, while they are text they are in an outdated file encoding, are counted as binary by git so merge and diff don't work. Make sure you convert the files before a commit - the file diff should show the changes clearly. Notepad++ can do the file encode conversion, though the built-in macro doesn't seem to work properly. I did a dumb method of using a mouse macro to send keystrokes of convert->save->close the files after opening up every one.
From this, make a new branch from translation for the merge. Then you merge and resolve conflicts from the mods. Once you do this setup once it is also very easy to keep things updated.