The relative thickness of the parts does not matter, I would not remove excessive material from one to match the other. Simply take a minimal clean up cut on both gasket surfaces to true them up. Then back spot face/reverse counterbore (you or the machine shop will have to buy the tool probably) the bolt/nut counterbores to make them flat from the intake to the exhaust. A bit harder and more expensive as you need the special back spot face tool and a complicated setup on a mill/drill, but this is the best way if you can find somebody to do it for you. Nice gasket surface and no split washer BS for a nice even clamping surface.
