I use a old Craftsman brand depth micrometer and rock the piston around while checking the deck height on both sides(cam side and then the motor mount side) of the pistons and the average the two measurements, all 8 of them
My micrometer base isn't wide enough to reach across most BB bores so I have to measure the edges up to around 3.75 bore size so the base has a decent seat to slide on
I also have and have used a magnetic base dial indicator bridge holder that will work on the bigger bores up to around 5.000 inch
When I use it I will slide it so it is over the wrist pins as close the cylinder bore sides and rock the pistons again from the front side end then slide the bridge back to the flywheel side of each cylinder and measure again when rocking and then average the two to get the deck height of all 8