QuoVadis is right, just place your own pk3's in the mod folder. This way peope will download the file automaticly. Yes the menu will only be visible once the correct mod is loaded, or once they connected to your server, but is it really needed that the main menu will be different for all your visitors?
I think if you want to force people do download a pk3 file from etmain to etmain folder, you have to exec the file in your server.cfg then. I never had a pk3 file placed in etmain to download in my own server (exept maps), but I guess it will work just the same as with maps. You exec your mapcycle also in your server.cfg, so server knows what to load, when. I guess you can tell the server to load any pk3 file placed in your etmain. Never did that, but thats what I would try.
But last question, do you know how to create a menu, since you cant use the menu of FA ofcourse. You can unpack it and watch it to learn, but if you create one yourself, all settings and images must be changed, so its a unique menu. The menu of FA is pretty advanced, I advise you to start with an easy file first and get that working.