Deck Height is where the piston sits in relation to the deck of the block at T.D.C. As the stroke, rod length and pin height of the piston are machined within tolerances, there can be a Stack-up affect. Easiest way is to use one cylinder as a comparator. Fit all piston and rod combinations to a cylinder and trying different combinations of pistons and rods to get the most even result. If one combo is slightly taller, fit it to the front, back and both sides of a V type engine, taking the measurements and recording them. If the pistons protrude from the bore the pistons will need to be machined. If down the deck of the block can be machined to the required Deck Height needed.