Hi,
The rubber bushings should be pressed into the holes on the cover, then the cap washers go over the rubber bushings, the "cap nut" then snugs the cover down. The rubber bushings should stop any seepage or oil mist from getting blown out of the two openings and making a mess of your beautiful cover! You should be able to snug the bushings in, they may be the wrong size, but I doubt it.
I use RTV to secure a cork gasket to the cover. When the RTV is set, I can repeatedly remove the cover to adjust valves or, just check on things. There may be other ways, but an old time LBC mechanic showed me this technique and I'm happy with it.