I've tried duplicating the zm_levelcommon_weapons file and deleting the weapons I don't want in my map, changing my GSC and CSC to connect to the edited file, yet when I test my map the weapons that I "restricted" are still in the box, any help?

You don't need to remove them from the map to remove them from the box.

Use this script made by MakeCents that gives you control over the box: Link - Download is in the description