I'd have the heads' deck milled then set the heads on head gaskets on the block then mockup/set the intake and its' gasket on there & see how far the port/bolt hole alignment is off then another trip to the machine shop to have the heads' intake faces' milled. It's not easy but later on when done & frying the tires cause you got every sub system dead on or near dead on (depending on the system) you'll have forgotten about the time/effort/occaisional aggravation that it took to get you there