The way I do it, is to put it on a surface plate and measure to the top of the WP and subtract 1/2 of that. That will get you accuracy of .0005.
Calipers, will get about .002 accuracy.
You can get close, if you accurately measure the stroke, C/C length of the rod and piston compression height. Then install them (that one assembly), in each cylinder and measure the deck clearance. The clearance in each item, will make it impossible to get exact figures but, you should be able to come within .003/.004. You can't assume anything when measuring things. The temperature, will also effect your measurements. The standard is 20C or 68F. I always had to do my close tolerance measurements, in a temp controlled room.
For examples, 390 and up rod, is 6.488 +/- .002. My Speed Pro pistons are suppose to be 1.660 and they are 1.6575