We straighten warped cylinder heads if possible. Generally speaking, if the bottom of the head is warped the top will be too, so both sides would need to be planed a bit. Minimum thickness is supped to be 84.00 mm, however, if the top of the head was milled that would lower your thickness but not affect your minimum clearances.
The only way to really know if a cylinder head is still good to use is to check the intake valve to piston clearance. The minimum clearance is .9 mm and this is checked by turning the crankshaft to 5 degrees ATDC on number 1 piston. This is the point where the piston and intake valve come the closest. Use a dial gauge and push down on the intake valve until it hits the top of the piston. As long as your gauge reads more than .035'' or .9 mm you will be OK. I save the old head gasket for making this measurement as you would certainly not want to use a new one just to make this measurement.
Since most head milling also involves a valve job you can expect that the valve seats will also be cut deeper which will also give you a bit more clearance. Having said that, it's important to remember that the intake valves require a minimum recession of .5 mm and the crushed head gasket is roughly 2 mm so in most cases you should have plenty of valve to piston clearance. It's also important to keep the rocker geometry correct or you can wipe out a new set of valve guides very quickly. I like a couple of threads showing on the ball stud or at least right at the start of the threads. If you have to adjust almost to the bottom of the hex that's too far in and I would recommend placing a .015'' shim under each cam bearing. This will raise the camshaft which will then give you enough adjustment on the ball studs. The cam shims will also help to remove any excess slack in the timing chain.
