Inthedirt, if you can't feel the gasket with your fingernail or a good razor blade knife, I'd ignore the visable look of a gasket there and don't do anything else with it and just move on, the stain left should not hinder the new gasket at all, remember the new gasket can't see the old stain but can feel if you'd cut some uneven excess metal out and leave a depression where it'll be prone to leak. I know of a lot of guys that can't accept the look of the stain and get carried away and when you cut and can see the swirl marks left by the disc or sanding pads its apparent they took off way too much, if you'd lay a straight edge on the flat surface and shine a light to see the spots that are cut too deep and let light under the straight edge you'd know its not level and a machined flat surface any longer. I've machined parts myself and know how to run the straight edge and also feeler guages and how to calculate how much material has been taken off and how much more needs to be machined off to get another flat service back on it.
Use the simple fingernail or razor blade test, its usually bullet proof unless you have a warped surface your dealing with to start with. I almost always lay a machinest straight edge over pieces to see how true and flat they are before reassembly, expecially if it'll take more than a few minutes to replace the gasket the second time around if it leaks but thats just me. Almost all machined surfaces have tollerances allowed before needing machining again, it depends on what and where they are and how used in the engine or component, the problem arises from die grinding with the discs is you never take the same amount off in any given area and in a few minutes you can take a perfectly acceptable surface within tollerance and turned it into one no gasket will keep sealed but it'll look nice and shiney with swirl marks and a excellant pollished mirror finish, just like it comes back from the machine shop with except, now its out of tollerance and the new gasket will never seal it up again.
The very best advice I was ever given was from a macinest one time and he told me this, "remember an engine can't see and gasket surfaces can't think, they only do one thing and thats seal, think of it like a making love to a woman with the lights out and use your fingers to determine the surface at hand not your eyes." I got quite a chuckle out it at the time but in the general gest of things maybe he was right. Before leaving he handed me a straight edge and told me to throw away my grinding discs and said if its smooth and level leave it alone, if not bring it in and I'll grind it so its right and ignore the look of it completely.