Chuck, You must, absolutely must, make sure it's on TDC when you measure. Also the pistons assemblies should remain in the holes you measured. So mark them with a cylinder number.
I'd prefer to see you check all eight holes, just to be sure, You can have material removed from the top of a piston if you find you need to. Suggest that you have the assembly balanced after you remove that material. Check the block with pistons that are fit to the block, loose ones can rock on the pin and throw your measurements off.