duTch is right, the head top face is unlikely to be the problem. To remedy any deviation properly on a fly cutter would need the valve guides to be removed, so is best left alone unless you can see major damage or deep scoring to the mating face. Otherwise it would entail milling along the faces, labour intensive, more expensive.
To see if the fault is head or box, remove the studs from the rocker box and place it on a sheet of glass...glass topped table, window glass etc, If it sits with no gaps or rock, the fault is in the head face. More likely the rocker box is the problem and the high spots will show themselves. A little bit of attention to carefully flatten them out should effect a cure for the leaks. If it proves too badly warped, a trip to your local engine reconditioner and a couple of minutes on a fly cutter will restore the faces. If this is required, only remove the minimum amount of material, its a bit crowded inside that rocker box. As musky says, make sure the corner stud threads are not raised, and aim for no rock when placed on the sheet of glass.
Swarfy.