I just dropped the Font1.pak into the location you pointed at and for some reason when i clicked Mods there's nothing there

Am i doing it right?
Main mod .pak-s that were created manually will not be visible in the Mods menu.
It doesn't matter however; the game engine will add the paths in the .pak even if you uncheck the checkbox next to a mod, it'll only prevent it from loading the Mods\%modName%\ stuff, but it won't prevent Mods\Main\ and Public\Main\ overrides from working.