You will want to set the height with the emulaters in, springs out and fully collapsed. Depending on what rate springs your using you will probably want to be between 4 & 5 inches from the top.
it would change the equation if you were to put in a measured volume of oil lets say 375cc then you would have to minus the volume that the emulators take up. but becuase you put the emulator in and take out oil to a measured ht. you are compensating for the added volume that it takes up. I would recommend 110mm for a oil ht.