@steed Although I think your way should have worked out if not for a small error (below), @bhepler 's advice is much better, because otherwise you will have a problem as soon as you want to update the mirror software.
The module’s own .js files themselves are part of the git workflow, if you change them locally and are not common to using git, you’ll be in a fine mess later on and will not know what to do.
Therefore, it’s ideal to use the config.js or custom.css for changes because they will be ignored by the git workflow.
However in your approach you have only one small mistake
The “~” leads to your home/pi directory therefore it was redundant and the system was looking for /home/pi/home/pi/…
OR just use this