Dimple the headers with a round pipe or socket where they get close. Use the 90 deg boots, As was said use the Accel Plugs. If you dimple with a hammer Or for that matter anything, Hold it solid and hit it with another hammer. This is a lot easier if the heater has been heated with a torch at the palce you want to dimple it. Don't go wild and crazy and just start beating on it. Correctly dimpled headers cause no restriction and still look good.
Ed