I make sure the crank rod journals have been equal stroked and indexed. then with the crank/main brgs in the block I install the same piston/rod combo at all four corner cylinders. Install piston w/o rings or some like to have the oil ring installed to add a little drag to the piston so it wont slide up/down too easily as you find tdc. Using magnetic dial indicator I find exact tdc of piston in each cylinder, then measure the distance piston is down the bore from deck surface. Like Rusty said the four measurements probably wont be the same. then have shop machine the block decks so they are parallel with crank centerline. after machine work I mockup the crank/piston again to verify all four corners have the same measurement...or at least real close.
