Milling the head gasket surface, commonly called the deck, on 4-stroke overhead cam style head should only be done to flatten a warped surface and not to increase compression. A warped head is usually the result of overheating and shows up as a blown head gasket between the bolts that hold down the head on each side of the exhaust. The gasket will usually allow coolant to leak from the water jacket into the combustion chamber rather than towards the outside the head were it would be visible. High compression pistons are available to gain the desired compression. Milling the deck reduces the distance between the cam sprocket and crank sprocket which slackens the cam chain. The extra chain length is taken up by the cam chain tensioner and rotates the cams in the direction of the tensioner which changes the cam timing. The same situation happens if thinner head or cylinder base gasket is installed. Most cam chain adjuster can only take up a small amount of slack associated with a worn chain. The higher compression from milling may give the desired compression but most likely the cam timing changes will have an adverse effect. Cams are available with adjustable slotted sprockets which can be set to the desired cam timing. This takes the knowledge of a skilled technician, a degree wheel and a dial indicator with a special holder. Not usually found in a back yards mechanics tool arsenal.
2-stroke head milling for compression is a standard engine builders service. That’s why you don’t see a lot of high compression pistons for 2-stokes. You can mill a 2-stroke head with not change in timing.
We mill lot of 4-stroke heads due to overheating, improper torque or head surface damage. Most of the time we can correct the warp by sanding it on a flat surface if it’s around .07mm or .003". Any more than that and we mill it. The amount we take off usually changes the timing about the same as a worn or stretched cam chain. Valve seat to guide concentricity may have to be corrected as the casting that hold the guides can also distort from overheating. If the bike is harder to start or the doesn’t seem to run properly after overheating this is probably why. A concentricity gauge that rotates around a guide pilot is required that reads in tenths of a thousandths for motocross heads. Warped heads are a result from running the motor after the coolant has boiled off. General thinking would assume the head gasket blew which sucked out the sucked coolant but its usually the other way around. Jigging up and holding a motocross head takes longer than the actual milling time. Fastheads.com charges $70 to $100 to surface mill and check the seat concentricity.