You'll need the new pistons in the block, the only really accurate way to get the deck height set correctly. The shop we use bores the block, fits the pistons to the pins and installs them without the rings to determine the amount of deck cut, then removes the rods and pistons, continues the machine work. Think I'd go with the measurements the shop comes up with as they are doing the machining rather then give them a predetermined set of measurements that may or may not be accurate to the actual dimensions of the new parts......

They can bore the block with the deck plates installed, take them off to set and cut the deck, then reinstall the plates to do the honing. Been awhile since I've worked an automotive machine shop, but I don't think the procedure has changed much.....