Really, you've just got to use an abrasive that's harder than gasket material, but softer than the cylinder head. I'm not afraid to use steel bristle wire brushes on iron, but I wouldn't use a steel bristle rotary tool. Brass wheels wear out fast, but they shouldn't hurt anything. The DIY thing is to scoot your cylinder head mating surface around on a piece of plate glass wrapped in emery cloth afterward. I used scrap glass from an antique aquarium. Marble or granite counter scrap would work. It's a sliding scale of how valuable your time is. You can take a long time and do it cheap or you can pay a machine shop to do it fast, or even not do it at all, but having taken it this far apart, I would face them.
NMWR 9-2815-274 : Using a straight edge and feeler gauge, check flatness of cylinder head to block mating surface. Flatness of cylinder head (11) must not vary more than 0.002-in. (0.051 mm) in distance of 6 in. (15.2 cm), or more than 0.006 in. (0.152 mm) overall. Replace cylinder head (11) if flatness does not meet specifications.