You can't put upgrades on the upgrades station GUI menu. That GUI is rendered client side, not server side. It's impossible to change that from the server.
The client buys upgrades from the GUI for each weapon, and the server merely verifies those upgrades that the client sends (to prevent stupid shit like crits on kill on minigun exploit). As for what shows up on the station yourself, your client displays that from its own files and doesn't ask the server for anything.
EDIT: With the gamerules entity you can set the custom upgrades station file but it is shitty and buggy to say the very least.
EDIT 2: This plugin looks like it needs to be rewritten from the ground up given the masses of errors everywhere.