Carefully tape over the mating surface on the underside of the head. Use something durable like duct tape. Take a small hand file and file all around the pilot nose on the cylinder head. Use care to keep the file parallel to the pilot nose and use continuous strokes and follow the curvature. If it's a really small amount of interference, this should work OK. You can clean the filings off and test fit the head as you go. You may only need to take it down a thousandth of an inch or so.
If you know someone with a metal lathe, they can chuck on a spark plug to spin the head. Careful dial indicator use and swapping around as they tighten the chuck should get it running perfectly true. Then it's just a matter of a very small cut (or it could filed down while in the lathe).
I'd go with the first method as it's easier to check the fit as you go. The cylinder can be off center by a couple of thou and have no detrimantal effect on the engine. The only really important thing is to keep the mating surface of the head (and the oring grooves) in good shape.
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2011 EC250E
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