Just let a machine shop do it. That will be the proper way to do the job. Have them check the heads' tolerances and they could surface it for you at the same time.
If your confident.....You could drill it with a hand drill, its only 1 mm. Make sure to flush your head with some sort of fluid repeatedly to clean the debris out. Also make sure to deburr the holes somehow so no schards of metal interfere with the sealing of your head gasket.
But 12.7mm is more than enough clearance for 12mm studs.