You would need to replace the box with one from a car w/o AC. Yes, the entire heating/cooling system goes through there. If you don't need heat, it'd be easier to pull the whole thing and block it with a flat plate.
I would call Vintage Air and find out if they have a kit for your car. I know htey have them for the first gen cars but I'm not sure about the gen two cars.
Their kits are very well thought out and they don't stick through the firewall.
Art Rasmussen Desgn and Fabrication, Inc. WWW.HOTRODDINGTODAY.COM