Plug a smog hole

Go to the hardware store, get 8 1/4-20 set screws 1/4 to 3/8 long, buy a 1/4-20 tap while you are there unless you already have a tap and die set. Tap the holes not quite the full length of the set screw, if you like you could use a little J-B Weld on the set screws, run them in and make them tight. Grind or flat file anything that sticks up till it's smooth. Done!
THIS ^^^^^ I put a drop of oil on the tap, and slowly go back and forth to let is slowly cut the threads and avoid breaking the tap off inside the head. I always go deep enough so that the set screw is just submerged below the surface. That way, no grinding, and your manifold/header will fit flat and seal proper. I've done this way more than I wish to remember, and never had anything go wrong. You'll do fine