Dudes! For one, never file a port surface, unless you have a really long file and a good eye. You'll end up making it worse. And two, the two studs come out easily when you know what you're doing.
2-double nut the stud with two nuts and lock them together with two wrenches(or vicegrips or whatever). Unscrew on the inner nut and it'll come out. Then,
1-using something flat(flat-steel, wood), wrap some sandpaper around it and sand with that. That will give you a much flatter surface than taking a file to it.
4-dragray had a good point, some copper rtv on the surfaces will ensure sealage, even for your metal gasket.
3-if you have an old leather boot, cut out a chunk of that to use for a gasket, bullet casings or hole punches can be used for the stud holes. Then clamp it on good once, and take it off. Now you have a perfect imprint of your ports to get out the exacto knife and have at it.
5-you can still rtv the leather to make sure the seal is good.
Don't forget to sand your exhaust flange with your flat surface, that'll help flattening both surfaces. While you have it off, is a good time to port match the flange the best you can, for better performance.
gl.