mite try to retorque the head/make sure the nuts and studs arent stripped before you yank it all apart. my engine lost compression immediatly after a few rides, and it was bcuz it had somehow stripped 4 case studs
otherwise if you're gonna tear it all down, do it rite-idk what engine it is, but id say new rings, hone the cylinders, new head gasket, valve job, new valve springs, use a straight edge and check that the head isnt warped, make sure no valves are bent....lots of performance stuff can be done at this time too, but you didnt ask that. may be able to get away with just doing a top end rebuild, but it wouldnt hurt to pull the crank, balance it, and check the bearings...
like i said, depends on the engine-maybe you can just pull the head, make sure its not warped, put a new head gasket on and be done with it.
i think im 4getting something, its like 315am, just got in, cant sleep, wired-back marker has built a bunch of engines2, im sure him or some1 else will correct me if i did 4get somethin